LiteFold/DisProt huggingface dataset:
Protein: DP02786 (UniProt Q9Y823)
Region: residues 320	to 333
Annotation: disorder to order (Structural transition)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the structures of the HCS apoenzyme and one of the 2-OG binary complexes, a lid motif from the C-terminal domain occludes the entrance to the active site of the neighboring monomer, whereas in the second 2-OG complex the lid is disordered, suggesting that it regulates substrate access to the active site through its apparent flexibility.
In the course of screening crystals of the SpHCS·2-OG complex, we identified two different conformations of the lid motif (residues 320–333) that encloses the entrance to the active site, which we term the closed and open conformations. In the closed lid complex (2.67 Å resolution), the lid motif is clearly visible in the electron density map and obstructs the entrance to the active site, whereas in the open complex (2.72 Å resolution), density for the lid is absent, resulting in a solvent-exposed active site.
Cross-references: PDB:3IVU
PDB:3IVT
Protein: DP02786 (UniProt Q9Y823)
Region: residues 320	to 333
Annotation: entropic chain (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the structures of the HCS apoenzyme and one of the 2-OG binary complexes, a lid motif from the C-terminal domain occludes the entrance to the active site of the neighboring monomer, whereas in the second 2-OG complex the lid is disordered, suggesting that it regulates substrate access to the active site through its apparent flexibility.
In the course of screening crystals of the SpHCS·2-OG complex, we identified two different conformations of the lid motif (residues 320–333) that encloses the entrance to the active site, which we term the closed and open conformations. In the closed lid complex (2.67 Å resolution), the lid motif is clearly visible in the electron density map and obstructs the entrance to the active site, whereas in the open complex (2.72 Å resolution), density for the lid is absent, resulting in a solvent-exposed active site.
Cross-references: PDB:3IVU
PDB:3IVT
PDB:3IVS
Protein: DP02787 (UniProt P45523)
Region: residues 26	to 39
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N and C termini of the FkpA polypeptide chain have peptide segments of 14 (in all three structures) and 18 residues (in full-length FkpA), respectively, which could not be identified in the electron density maps of the crystal structures.
Cross-references: PDB:1Q6I
PDB:1Q6H
PDB:1Q6U
Protein: DP02787 (UniProt P45523)
Region: residues 15	to 114
Annotation: protein folding chaperone (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
These results suggest that the chaperone and catalytic activities reside in the N and C-terminal domains, respectively.
Cross-references: PDB:1Q6I
PDB:1Q6H
PDB:1Q6U
Protein: DP02787 (UniProt P45523)
Region: residues 253	to 270
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N and C termini of the FkpA polypeptide chain have peptide segments of 14 (in all three structures) and 18 residues (in full-length FkpA), respectively, which could not be identified in the electron density maps of the crystal structures.
Cross-references: PDB:1Q6U
Protein: DP02787 (UniProt P45523)
Region: residues 253	to 270
Annotation: disorder to order (Structural transition)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N and C termini of the FkpA polypeptide chain have peptide segments of 14 (in all three structures) and 18 residues (in full-length FkpA), respectively, which could not be identified in the electron density maps of the crystal structures.
Accordingly, the observed mobility of the C-terminal domains of the dimeric molecule could effectively adapt these two independent folding functions of FkpA to polypeptide substrates.
The C-domain (residues 115–224) belongs to the FKBP family. This domain has an FK506-binding site characteristic of this protein family, fixing the ligand in the same manner as observed in other FKBP structures that have been determined.
Cross-references: PDB:1Q6U
PDB:1Q6I
Protein: DP02789 (UniProt Q62902)
Region: residues 31	to 49
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 31–49 and the 6xHis tag inserted between residues 34 and 35 (23) are not visible in the electron density maps.
The final model contains residues 50–277 of p58, 197 water molecules and 2 sulfate ions.
Cross-references: PDB:1GV9
Protein: DP02790 (UniProt Q8BTI9)
Region: residues 1	to 12
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The structure of p110β has residues 1-12, 228-234, 299-319, 402-431, 514-524 and 1058-1064 disordered.
Cross-references: PDB:2Y3A
Protein: DP02790 (UniProt Q8BTI9)
Region: residues 299	to 319
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The structure of p110β has residues 1-12, 228-234, 299-319, 402-431, 514-524 and 1058-1064 disordered.
Cross-references: PDB:2Y3A
Protein: DP02790 (UniProt Q8BTI9)
Region: residues 402	to 431
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The structure of p110β has residues 1-12, 228-234, 299-319, 402-431, 514-524 and 1058-1064 disordered.
Cross-references: PDB:2Y3A
Protein: DP02790 (UniProt Q8BTI9)
Region: residues 514	to 524
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The structure of p110β has residues 1-12, 228-234, 299-319, 402-431, 514-524 and 1058-1064 disordered.
Cross-references: PDB:2Y3A
Protein: DP02790 (UniProt Q8BTI9)
Region: residues 299	to 319
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Flexible linker connecting RBD domain and C2 domain
Cross-references: PDB:2Y3A
Protein: DP02791 (UniProt O08908)
Region: residues 423	to 440
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The regulatory p85β structure has residues 423-440, 501-507, 576-607 and 715-722 disordered.
Cross-references: PDB:2Y3A
Protein: DP02791 (UniProt O08908)
Region: residues 576	to 607
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The regulatory p85β structure has residues 423-440, 501-507, 576-607 and 715-722 disordered.
Cross-references: PDB:2Y3A
Protein: DP02791 (UniProt O08908)
Region: residues 423	to 440
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Flexible linker connecting nSH2 domain and iSH2 domain
Cross-references: PDB:2Y3A
Protein: DP02791 (UniProt O08908)
Region: residues 576	to 607
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Flexible linker connecting iSH2 domain and cSH2 domain
Cross-references: PDB:2Y3A
Protein: DP02791 (UniProt O08908)
Region: residues 576	to 607
Annotation: phosphorylation display site (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Another conserved Tyr modified by phosphorylation is in the iSH2-cSH2 linker
(Tyr607-Hsp85α, Tyr605-Hsp85β, Tyr341-Hsp55γ, Tyr599-Mmp85β).
Cross-references: PDB:2Y3A
Protein: DP02792 (UniProt P42337)
Region: residues 310	to 322
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Flexible linker between RBD domain and C2 domain
Cross-references: PDB:4A55
Protein: DP02792 (UniProt P42337)
Region: residues 310	to 322
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Flexible linker between RBD domain and C2 domain
Cross-references: PDB:4A55
Protein: DP02792 (UniProt P42337)
Region: residues 501	to 525
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Flexible linker between C2 domain and PIK domain
Cross-references: PDB:4A55
Protein: DP02792 (UniProt P42337)
Region: residues 501	to 525
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Flexible linker between C2 domain and PIK domain
Cross-references: PDB:4A55
Protein: DP02793 (UniProt Q63716)
Region: residues 176	to 199
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The C-terminal ≈20 residues of HBP23 corresponding to the N-terminal half of this ORF6 subdomain are disordered in the crystal as described.
The current structure of HBP23 consists of 173 residues (3–175); the N-terminal 2 and the C-terminal 24 residues (176–199) are not included in the model because of their weak electron densities.
Cross-references: PDB:1QQ2
Protein: DP02794 (UniProt P22234)
Region: residues 37	to 51
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Several regions of the polypeptide chain, including residues Met1–Val6, Asp37–Glu51, and Asp221–Thr238, were not visible in the electron density map and assumed being disordered in the crystal.
All three above-mentioned disordered regions in the PAICS crystal structure are located in the SAICARs domain.
Cross-references: PDB:2H31
Protein: DP02794 (UniProt P22234)
Region: residues 221	to 238
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Several regions of the polypeptide chain, including residues Met1–Val6, Asp37–Glu51, and Asp221–Thr238, were not visible in the electron density map and assumed being disordered in the crystal.
All three above-mentioned disordered regions in the PAICS crystal structure are located in the SAICARs domain.
Cross-references: PDB:2H31
Protein: DP02795 (UniProt Q9NV23)
Region: residues 1	to 24
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model only contained residues 25–58, 77–158, and 166–265.
Cross-references: PDB:4XJV
Protein: DP02795 (UniProt Q9NV23)
Region: residues 59	to 76
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model only contained residues 25–58, 77–158, and 166–265.
The remaining coil and short helical sections of the capping domain and the backside of the molecule exhibit 2–3-fold higher B-values or are missing in the electron density (residues 59–76 and 159–165).
Cross-references: PDB:4XJV
Protein: DP02796 (UniProt Q56026)
Region: residues 111	to 131
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The crystal structures of SipD in the apo and bound forms are nearly identical (Fig. 1 and Supporting Information Fig. S2). For the SipD-deoxycholate crystal (Fig. 1), the final model includes residues 39-342 for molecule A and 46-336 for molecule B. However, residues 110-132 in molecule A and residues 92-94 and 118-134 in molecule B can not be fit to the electron density due to disorder.
Cross-references: PDB:3NZZ
Protein: DP02796 (UniProt Q56026)
Region: residues 1	to 21
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In SipD crystals, as in the crystal structures of IpaD [16] and BipD [17], the N-terminal 31, 38 or 29 amino acids, respectively, were not defined.
Protein: DP02796 (UniProt Q56026)
Region: residues 1	to 21
Annotation: flexible N-terminal tail (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In SipD crystals, as in the crystal structures of IpaD [16] and BipD [17], the N-terminal 31, 38 or 29 amino acids, respectively, were not defined.
Protein: DP02797 (UniProt P20061)
Region: residues 318	to 330
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In contrast to the crystal structure of human TC, the HC linker does not participate in crystal contacts over its full length and is largely disordered (residues 296–307).
It comprises two globular domains, the N-terminal α-domain (residues 1–287) and the C-terminal β-domain (residues 309–410), which are connected by a flexible linker
Flexible linker between cobalamin binding domain and globular c-terminal beta domain. Residue numbers in the publication refer to multiple sequence alignment in Figure 2 and not to the protein sequence.
Cross-references: PDB:4KKJ
PDB:4KKI
Protein: DP02797 (UniProt P20061)
Region: residues 318	to 330
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In contrast to the crystal structure of human TC, the HC linker does not participate in crystal contacts over its full length and is largely disordered (residues 296–307).
It comprises two globular domains, the N-terminal α-domain (residues 1–287) and the C-terminal β-domain (residues 309–410), which are connected by a flexible linker
Flexible linker between cobalamin binding domain and globular c-terminal beta domain. Residue numbers in the publication refer to multiple sequence alignment of Figure 2 and not to the protein sequence.
Cross-references: PDB:4KKJ
PDB:4KKI
Protein: DP02797 (UniProt P20061)
Region: residues 1	to 23
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows this region lacks electron density, indicating it is disordered.
Cross-references: PDB:4KKJ
PDB:4KKI
Protein: DP02798 (UniProt P23771)
Region: residues 304	to 314
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The linker region in all three crystal structures shows a large flexibility as evident by high B-factors and a weak electron density.
Cross-references: PDB:4HCA
Protein: DP02798 (UniProt P23771)
Region: residues 304	to 314
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The linker region in all three crystal structures shows a large flexibility as evident by high B-factors and a weak electron density.
These structural analyses suggest that the linker region between the N-finger and the C-finger in GATA3 does not appear to have any conformational limitations. One of its functional roles appears to be providing a constraint on the spacing of the palindromic sites and the geometric distance between the DNA molecules bridged by GATA, while the flexibility of the linker region allows a wide variety of orientations of the bridged DNA molecules.
Cross-references: PDB:4HCA
Protein: DP02798 (UniProt P23771)
Region: residues 304	to 314
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The linker region in all three crystal structures shows a large flexibility as evident by high B-factors and a weak electron density.
Cross-references: PDB:4HCA
Protein: DP02799 (UniProt P34257)
Region: residues 104	to 135
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
All DNA bases and amino acid residues 2–103 were defined in electron density, but electron density for amino acid residues 1 and 104–135, and the C-terminal His-tag is missing.
The structure reveals two helix–turn–helix (HTH) protein domains separated by a linker of 18 amino acids, binding to the 26mer duplex of DNA, as shown in Figure ​Figure2.2. All DNA bases and amino acid residues 2–103 were defined in electron density, but electron density for amino acid residues 1 and 104–135, and the C-terminal His-tag is missing. It is probable that the N-terminal methionine was removed from the protein, as shown for the earlier construct (17). The C-terminal residues are not visible in the electron density, probably due to the flexibility of these amino acids in the absence of the catalytic domain.
The limited resolution, the high B-factor of the data and the missing C-terminal amino acids result in a relatively high R-factor (23.3%) and free R-factor (27.3%).
Cross-references: PDB:1U78
Protein: DP02800 (UniProt P63028)
Region: residues 39	to 66
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 1–38 and 68–170, and 1–41 and 67–170 were modeled for chains A and B, respectively; similar to other crystal structures of HRF (Vedadi et al., 2007, Susini et al., 2008, Dong et al., 2009, Eichhorn et al., 2013), the mobile loop region (residues Thr39-Val66) was disordered.
Cross-references: PDB:5O9K
Protein: DP02800 (UniProt P63028)
Region: residues 39	to 66
Annotation: molecular function regulator (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
HRF crystal and solution structures have provided little insight into either the formation of disulphide-linked HRF dimers or the ability of HRF to activate mast cells.
The current model for the activity of HRF in mast cell activation involves cross-linking of FcεRI-bound IgE by dimeric HRF, mediated by interactions between HRF and the Fab regions of IgE
Cross-references: PDB:5O9K
Protein: DP02801 (UniProt P05452)
Region: residues 22	to 46
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N‐terminal 25 residues can not be located in the electron density maps, indicating disorder in the N‐terminal part of TN.
The disordered segment at the N-terminal region of the protein correspond to residues 22-46, since region 1-21 is the signal peptide
Cross-references: PDB:1HTN
Protein: DP02801 (UniProt P05452)
Region: residues 1	to 49
Annotation: protein binding (Molecular function)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
The close structural resemblance of TN to the neck and CRD part of the MBPs, where carbohydrate‐binding is conferred to the CRD, whereas other additional domains provide the diversity of functions of these proteins, indicate that the kringle 4‐binding site resides within residues 1–49 of the TN sequence. This is supported by the observation that only the full‐length protein and not the isolated CRD binds to immobilized kringle 4 (Holtet, T.L., unpublished). 
However, the observations that TN binds to the kringle 4 domain of plasminogen [1, 10], interacts in a calcium‐dependent manner with sulfated polysaccharides [11] and fibrin [12], binds to immobilized fucoidan (Graversen, J.H., unpublished), as well as the presence of two characteristic calcium sites in the TN structure, suggest that one function of the protein is to target plasminogen to specific carbohydrate ligands on cell surfaces, in the extracellular matrix or to fibrin.
Cross-references: PDB:1HTN
Protein: DP02801 (UniProt P05452)
Region: residues 1	to 49
Annotation: localization (Biological process)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
The close structural resemblance of TN to the neck and CRD part of the MBPs, where carbohydrate‐binding is conferred to the CRD, whereas other additional domains provide the diversity of functions of these proteins, indicate that the kringle 4‐binding site resides within residues 1–49 of the TN sequence. This is supported by the observation that only the full‐length protein and not the isolated CRD binds to immobilized kringle 4 (Holtet, T.L., unpublished). 
However, the observations that TN binds to the kringle 4 domain of plasminogen [1, 10], interacts in a calcium‐dependent manner with sulfated polysaccharides [11] and fibrin [12], binds to immobilized fucoidan (Graversen, J.H., unpublished), as well as the presence of two characteristic calcium sites in the TN structure, suggest that one function of the protein is to target plasminogen to specific carbohydrate ligands on cell surfaces, in the extracellular matrix or to fibrin.
Cross-references: PDB:1HTN
Protein: DP02802 (UniProt Q921Z5)
Region: residues 1	to 12
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Except for 12 flexible N-terminal residues (Met1-Ala12), all other amino acids are defined in the electron density map.
Cross-references: PDB:5JXD
Protein: DP02802 (UniProt Q921Z5)
Region: residues 1	to 12
Annotation: small molecule binding (Molecular function)
Evidence: protein mass spectrometry evidence used in manual assertion
Supporting statements:
Our structural analysis suggests that the flexibility of the N-terminal domain together with the described positively charged surface (Fig. 4) may be important for the biological functions of mTnfaip8 and hTIPE3 probably assisting in the uptake and release of phosphoglycerides.
Cross-references: PDB:5JXD
Protein: DP02802 (UniProt Q921Z5)
Region: residues 1	to 12
Annotation: molecular sequestering activity (Molecular function)
Evidence: protein mass spectrometry evidence used in manual assertion
Supporting statements:
Our structural analysis suggests that the flexibility of the N-terminal domain together with the described positively charged surface (Fig. 4) may be important for the biological functions of mTnfaip8 and hTIPE3 probably assisting in the uptake and release of phosphoglycerides.
Cross-references: PDB:5JXD