LiteFold/DisProt huggingface dataset:
Protein: DP02420 (UniProt Q86YV5)
Region: residues 1030	to 1039
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The majority of the residues were visible in the structure with the exception of residues present in surface exposed loops: 932–943, 977–983, 1030–1039, 1065–1081, 1159–1207, 1218–1238 and 1336–1345.
Cross-references: PDB:5VE6
Protein: DP02420 (UniProt Q86YV5)
Region: residues 1065	to 1081
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The majority of the residues were visible in the structure with the exception of residues present in surface exposed loops: 932–943, 977–983, 1030–1039, 1065–1081, 1159–1207, 1218–1238 and 1336–1345.
Cross-references: PDB:5VE6
Protein: DP02420 (UniProt Q86YV5)
Region: residues 1218	to 1238
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The majority of the residues were visible in the structure with the exception of residues present in surface exposed loops: 932–943, 977–983, 1030–1039, 1065–1081, 1159–1207, 1218–1238 and 1336–1345.
Cross-references: PDB:5VE6
Protein: DP02420 (UniProt Q86YV5)
Region: residues 1336	to 1345
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The majority of the residues were visible in the structure with the exception of residues present in surface exposed loops: 932–943, 977–983, 1030–1039, 1065–1081, 1159–1207, 1218–1238 and 1336–1345.
Cross-references: PDB:5VE6
Protein: DP02421 (UniProt O94687)
Region: residues 426	to 436
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Secondary structure alignment of the TAM-containing Te1 construct (426−545) used for the crystallographic study. Dotted line denotes the unmodeled parts of Te1 in the solved crystal structure due to their high flexibility.
In the solved structures from both crystal forms, approximately eight to ten residues from the N terminus and one residue from the C terminus were not modeled due to high flexibility and lack of sufficient density.
Cross-references: PDB:3D1B
PDB:3D1D
Protein: DP02421 (UniProt O94687)
Region: residues 117	to 452
Annotation: disorder (Structural state)
Evidence: author inference used in manual assertion
Supporting statements:
Although ARGONAUTE-interacting proteins might possess well-conserved and highly structured domains, such as the polymerase domains in NRPE1, AGO-binding platforms generally have poor sequence conservation between species and are intrinsically disordered [2, 6, 9,10,11,12].
The repetitive sequence units tend to contain at least one AGO hook and are enriched in disorder-promoting amino acids that contribute to the intrinsic disorder of the region [12].
The argonaute hook domain comprises the 117-452 protein region according to Pfam (PF10427).
Protein: DP02422 (UniProt O35254)
Region: residues 1	to 11
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Crystals of GRASP65 were obtained ~1 month after the crystallization setup. A 2.2-Å dataset was collected, and the structure was determined by molecular replacement (Table 1), but only residues 12–210 were visible in the electron density.
Cross-references: PDB:4KFV
Protein: DP02423 (UniProt Q5RJI5)
Region: residues 592	to 603
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
the isolated AIS sequence is highly flexible and solvent-accessible
Here, we report the crystal structure of the mouse SAD-B C-terminal fragment including the AIS and the kinase-associated domain 1 (KA1) at 2.8 Å resolution. The KA1 domain is structurally conserved, while the isolated AIS sequence is highly flexible and solvent-accessible. Our biochemical studies indicated that the SAD-B AIS exerts the same autoinhibitory role as that in SAD-A. We believe that the flexible isolated AIS sequence is readily available for interaction with KD-UBA and thus inhibits SAD-B activity.
the free AIS sequence in SAD-B is highly flexible, accessible to the KD-UBA interaction.
our results revealed the flexible shift of AIS between the free state and the inhibitory state, implicating its regulatory role for controlling the kinase activity.
the AIS sequence is largely flexible in isolated the AIS-KA1 fragment and readily available to interact with the KD-UBA domain, thereby inhibiting the SAD activity.
The structural analyses indicated that the isolated AIS sequence is largely flexible and solvent accessible, and that AIS in the AIS-KA1 fragment is readily available for binding to the KD-UBA junction and inhibiting the SAD activity.
Taken together, the AIS sequence of SAD-B is flexible in the isolated state and characterized by the autoinhibitory role.
Our recent study of mouse SAD-A identified a unique autoinhibitory sequence (AIS), which binds at the junction of the kinase domain (KD) and the ubiquitin-associated (UBA) domain and exerts autoregulation in cooperation with UBA.
Cross-references: PDB:5IRI
Protein: DP02423 (UniProt Q5RJI5)
Region: residues 592	to 603
Annotation: self-inhibition (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
the isolated AIS sequence is highly flexible and solvent-accessible
Here, we report the crystal structure of the mouse SAD-B C-terminal fragment including the AIS and the kinase-associated domain 1 (KA1) at 2.8 Å resolution. The KA1 domain is structurally conserved, while the isolated AIS sequence is highly flexible and solvent-accessible. Our biochemical studies indicated that the SAD-B AIS exerts the same autoinhibitory role as that in SAD-A. We believe that the flexible isolated AIS sequence is readily available for interaction with KD-UBA and thus inhibits SAD-B activity.
the free AIS sequence in SAD-B is highly flexible, accessible to the KD-UBA interaction.
our results revealed the flexible shift of AIS between the free state and the inhibitory state, implicating its regulatory role for controlling the kinase activity.
the AIS sequence is largely flexible in isolated the AIS-KA1 fragment and readily available to interact with the KD-UBA domain, thereby inhibiting the SAD activity.
The structural analyses indicated that the isolated AIS sequence is largely flexible and solvent accessible, and that AIS in the AIS-KA1 fragment is readily available for binding to the KD-UBA junction and inhibiting the SAD activity.
Taken together, the AIS sequence of SAD-B is flexible in the isolated state and characterized by the autoinhibitory role.
Our recent study of mouse SAD-A identified a unique autoinhibitory sequence (AIS), which binds at the junction of the kinase domain (KD) and the ubiquitin-associated (UBA) domain and exerts autoregulation in cooperation with UBA.
Cross-references: PDB:5IRI
Protein: DP02423 (UniProt Q5RJI5)
Region: residues 592	to 603
Annotation: molecular function inhibitor activity (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Here, we report the crystal structure of the mouse SAD-B C-terminal fragment including the AIS and the kinase-associated domain 1 (KA1) at 2.8 Å resolution. The KA1 domain is structurally conserved, while the isolated AIS sequence is highly flexible and solvent-accessible. Our biochemical studies indicated that the SAD-B AIS exerts the same autoinhibitory role as that in SAD-A. We believe that the flexible isolated AIS sequence is readily available for interaction with KD-UBA and thus inhibits SAD-B activity.
Cross-references: PDB:5IRI
Protein: DP02426 (UniProt Q80VW5)
Region: residues 420	to 430
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
However, the first 12 N‐terminal residues are not visible in the electron density of the dimer, indicating increased disorder or conformational heterogeneity of helix α1 compared to the five‐helix structure.
Cross-references: PDB:6FDE
PDB:6FDD
Protein: DP02427 (UniProt Q9BVI0)
Region: residues 70	to 85
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Strong electron density was apparent for residues 4–69. Terminal residues were disordered and without supporting electron density.
Cross-references: PDB:3QII
PDB:3Q1J
Protein: DP02428 (UniProt Q5T4W7)
Region: residues 108	to 120
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The amino-terminal 12 residues are disordered in each monomer; both monomers start at residue 13
Cross-references: PDB:2ASK
Protein: DP02429 (UniProt Q9WTY2)
Region: residues 137	to 150
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The absence of electron density suggests that switches I and II are disordered.
Overall, our structure reveals that switch I and switch II of Rem2 are flexible regions in the GDP-bound form and in the absence of the N- and C-terminal extensions.
Our analysis supports the idea that the crystal-packing environment stabilizes or imposes a conformation on the switch regions and that the switch regions are disordered in the absence of contact.
Differences in the crystal-packing environment revealed that the switch I and switch II regions are flexible and not ordered as previously reported
No defined electron density was observed in the switch I and II regions, i.e. residues 137–150 and 171–182 of molecule A, and residues 138–149 and 171–182 of molecule B.
Cross-references: PDB:4AII
Protein: DP02429 (UniProt Q9WTY2)
Region: residues 171	to 182
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The absence of electron density suggests that switches I and II are disordered.
Overall, our structure reveals that switch I and switch II of Rem2 are flexible regions in the GDP-bound form and in the absence of the N- and C-terminal extensions.
Our analysis supports the idea that the crystal-packing environment stabilizes or imposes a conformation on the switch regions and that the switch regions are disordered in the absence of contact.
Differences in the crystal-packing environment revealed that the switch I and switch II regions are flexible and not ordered as previously reported
No defined electron density was observed in the switch I and II regions, i.e. residues 137–150 and 171–182 of molecule A, and residues 138–149 and 171–182 of molecule B.
Cross-references: PDB:4AII
Protein: DP02431 (UniProt P15391)
Region: residues 138	to 152
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 118–185 form a three‐stranded β‐sheet of mixed topology (strands I, J, K) and two presumably unstructured partially disordered loops.
Residues 138–152 and 177–183 are not defined in the electron density and were not included in the model.
Cross-references: PDB:6AL5
Protein: DP02445 (UniProt Q96RS0)
Region: residues 618	to 633
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 634–844 of monomer 1 are well defined in the electron density map, whereas for monomers 2 and 3 only the residues 637–847 and 641–847 could be placed.
Cross-references: PDB:3GDH
Protein: DP02446 (UniProt Q8IU57)
Region: residues 270	to 299
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Beyond Ser270, the electron density for IFNLR1 is poor, suggesting disorder of the peptide backbone likely due to a lack of contacts with JAK1. In addition, we were unable to model the IFNLR1 box2 motif due to significant structural disorder in the JAK1 SH2 domain.
IFNLR1 box2 containing peptide (residues 270–299) showed no detectable binding to JAK1
Cross-references: PDB:5IXD
PDB:5IXI
Protein: DP02448 (UniProt Q03707)
Region: residues 196	to 221
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The crystal structure of ΔIBB-Kap60 crystallized in complex with a 50-mer spanning Heh1 resides 171-221 has density only for the first half of the Heh1 construct (residues 173-195), while no discernable electron density was observed for residues 196-221.
it was shown that a region between residues 173-220, encoding several basic patches similar to a cNLS, and a ~200 residues unfolded linker were required and sufficient for nuclear import
Cross-references: PDB:4XZR
Protein: DP02448 (UniProt Q03707)
Region: residues 222	to 454
Annotation: disorder (Structural state)
Evidence: author statement used in manual assertion
Supporting statements:
Sufficient for efficient import to the INM are the high-affinity NLS of Heh2 (h2NLS) or Heh1 and a long intrinsically disordered linker (L) between the NLS and the transmembrane domain. The disordered linker needs to be longer than 120 residues but no specific amino acid sequence is required.
Protein: DP02448 (UniProt Q03707)
Region: residues 222	to 454
Annotation: disorder (Structural state)
Evidence: author statement used in manual assertion
Supporting statements:
More recently, it was found (Meinema et al., 2011) that the NLS together with an intrinsically disordered (ID) linker ∼180–230 amino acids long in the extra-luminal surface of Heh1 and Heh2 is essential and sufficient for INM targeting.
The exact boundaries of the Heh1 NLS were unknown before this study, although it was shown that a region between residues 173 and 220, encoding several basic patches similar to a cNLS, and a ∼200-residue unfolded linker were required and sufficient for nuclear import (Meinema et al., 2011). 
Considering that a NLS domain was describe for the region 171–220 and the transmembrane region starts at the 455 residue, the authors are referring to the 221-454 region as the flexible linker region.
Protein: DP02448 (UniProt Q03707)
Region: residues 222	to 454
Annotation: flexible linker (Disorder function)
Evidence: author statement used in manual assertion
Supporting statements:
More recently, it was found (Meinema et al., 2011) that the NLS together with an intrinsically disordered (ID) linker ∼180–230 amino acids long in the extra-luminal surface of Heh1 and Heh2 is essential and sufficient for INM targeting.
The exact boundaries of the Heh1 NLS were unknown before this study, although it was shown that a region between residues 173 and 220, encoding several basic patches similar to a cNLS, and a ∼200-residue unfolded linker were required and sufficient for nuclear import (Meinema et al., 2011). 
Considering that a NLS domain was describe for the region 171–220 and the transmembrane region starts at the 455 residue, the authors are referring to the 221-454 region as the flexible linker region.
Protein: DP02449 (UniProt Q15583)
Region: residues 150	to 167
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 168–234 (chain A), 164–229 (chain B), and the 16mer dsDNA are well-defined in the electron density map
Cross-references: PDB:6FQP
Protein: DP02449 (UniProt Q15583)
Region: residues 235	to 248
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 168–234 (chain A), 164–229 (chain B), and the 16mer dsDNA are well-defined in the electron density map
Cross-references: PDB:6FQP
Protein: DP02449 (UniProt Q15583)
Region: residues 256	to 347
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The TGIF1 C-term domain is intrinsically disordered in solution
Cross-references: BMRB:27461
Protein: DP02449 (UniProt Q15583)
Region: residues 256	to 347
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The TGIF1 C-term domain is intrinsically disordered in solution
We found weak-medium interactions between the phosphorylated TGIF1 C-term and Smad2 linker-MH2 construct
We have shown how two distinct regions of TGIF1, namely the HD and the C-term domain, interact with the MH1 and MH2 domains of Smad proteins respectively.
We propose that the binding of the TGIF1 C-term to the Smad2-MH2 domain brings both the HD and MH1 domain into close proximity.
Cross-references: BMRB:27461
Protein: DP02449 (UniProt Q15583)
Region: residues 284	to 288
Annotation: phosphorylation display site (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The TGIF1 C-term domain is intrinsically disordered in solution
The C-term domain of TGIF1 holds the Smad-binding domain, which includes several phosphorylatable residues. Three of these residues, Ser286, 291 and 294, are phosphorylated in vivo, although the specific roles of these phosphorylations are not fully understood.
Cross-references: BMRB:27461
Protein: DP02449 (UniProt Q15583)
Region: residues 289	to 293
Annotation: phosphorylation display site (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The TGIF1 C-term domain is intrinsically disordered in solution" Results "The C-term domain of TGIF1 holds the Smad-binding domain, which includes several phosphorylatable residues. Three of these residues, Ser286, 291 and 294, are phosphorylated in vivo, although the specific roles of these phosphorylations are not fully understood.
Protein: DP02449 (UniProt Q15583)
Region: residues 292	to 296
Annotation: phosphorylation display site (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The TGIF1 C-term domain is intrinsically disordered in solution" Results "The C-term domain of TGIF1 holds the Smad-binding domain, which includes several phosphorylatable residues. Three of these residues, Ser286, 291 and 294, are phosphorylated in vivo, although the specific roles of these phosphorylations are not fully understood.
Protein: DP02451 (UniProt P46938)
Region: residues 35	to 64
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 chains are not visible in the electron density map and are assumed to be disordered;
residue chain B: 35–46 and 87–92; chain D: 35–47 and 83–92; chain F: 35–47 and 84–92; and chain H: 35–64 and 84–92.
annotated positions are referred to chain H
Cross-references: PDB:3JUA
Protein: DP02452 (UniProt Q8TEA8)
Region: residues 152	to 209
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The C-terminal portion of DUE-B (amino acids 152–209) is not visible in the crystal structure and is predicted to be dynamically disordered
We further demonstrate that the C-terminal portion of the enzyme is disordered and not essential for dimerization. However, this region is essential for DNA binding in vitro and becomes ordered in the presence of DNA. 
Cross-references: PDB:2OKV
Protein: DP02452 (UniProt Q8TEA8)
Region: residues 152	to 209
Annotation: DNA binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The C-terminal portion of DUE-B (amino acids 152–209) is not visible in the crystal structure and is predicted to be dynamically disordered
We further demonstrate that the C-terminal portion of the enzyme is disordered and not essential for dimerization. However, this region is essential for DNA binding in vitro and becomes ordered in the presence of DNA. 
The C-terminal residues that are involved in mediating interactions with target DNA are largely disordered in the crystal
the C terminus is necessary for binding of purified DUE-B to DNA.
Disordered regions of DNA-binding proteins often become ordered upon DNA binding
Cross-references: PDB:2OKV
Protein: DP02452 (UniProt Q8TEA8)
Region: residues 152	to 209
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The C-terminal portion of DUE-B (amino acids 152–209) is not visible in the crystal structure and is predicted to be dynamically disordered
We further demonstrate that the C-terminal portion of the enzyme is disordered and not essential for dimerization. However, this region is essential for DNA binding in vitro and becomes ordered in the presence of DNA. 
The C-terminal residues that are involved in mediating interactions with target DNA are largely disordered in the crystal
the C terminus is necessary for binding of purified DUE-B to DNA.
Disordered regions of DNA-binding proteins often become ordered upon DNA binding
Cross-references: PDB:2OKV
Protein: DP02455 (UniProt Q9UKX7)
Region: residues 48	to 109
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Finally, residues 48–109 were not visible in the crystal structure, although they were present in the crystal. This region contains 15 glycines and is likely highly flexible.
Cross-references: PDB:3TJ3
Protein: DP02456 (UniProt O35625)
Region: residues 1	to 17
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Electron densities of two Axin1 segments, Axin1(18-30) and Axin1(60-79), can be clearly visualized on the two ARC2 surfaces in the swapped TNKS dimers (Fig. S4). While the remaining parts of Axin1 cannot be seen in the electron density maps, these two Axin1 segments are likely from the same Axin1(1-80) molecule, since SEC results indicate that Axin1(1-80) stabilizes TNKS(308-655) dimerization in solution (Fig. S3), most likely by interacting with both copies of the swapped dimer. In addition, the distance between Axin1 G30 and A60 Cα atoms in our structure is 49.4 Å, which can be covered by the 29 missing residues in between
Cross-references: PDB:3UTM