LiteFold/DisProt huggingface dataset:
Protein: DP02669 (UniProt Q57530)
Region: residues 164	to 184
Annotation: protein binding (Molecular function)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
In this study, we report that 6b interacts with the tobacco nuclear protein NtSIP2, whose predicted sequence is significantly similar to that of the TNP1 protein, which is encoded by the transposable element Tam1 of Antirrhinum majus. Most NtSIP2 localizes to the nucleoli, and 6b localizes to a subnucleolar region as well as the nucleoplasm, suggesting their functions in the nucleolus; 6b could act as a histone chaperone similar to the nucleolar histone chaperones of animal cells, nucleophosmin/B23 and nucleolin.
Mutant AK6bΔA that lacked the acidic region did not bind NtSIP2 (unpublished data).
Protein: DP02669 (UniProt Q57530)
Region: residues 164	to 184
Annotation: localization (Biological process)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
In this study, we report that 6b interacts with the tobacco nuclear protein NtSIP2, whose predicted sequence is significantly similar to that of the TNP1 protein, which is encoded by the transposable element Tam1 of Antirrhinum majus. Most NtSIP2 localizes to the nucleoli, and 6b localizes to a subnucleolar region as well as the nucleoplasm, suggesting their functions in the nucleolus; 6b could act as a histone chaperone similar to the nucleolar histone chaperones of animal cells, nucleophosmin/B23 and nucleolin.
Mutant AK6bΔA that lacked the acidic region did not bind NtSIP2 (unpublished data).
Protein: DP02669 (UniProt Q57530)
Region: residues 164	to 184
Annotation: protein folding chaperone (Molecular function)
Evidence: enzymatic activity assay evidence used in manual assertion
Supporting statements:
Protein 6b Has Histone Chaperone–Like Activity
To examine the putative histone chaperone activity of 6b, we first performed supercoiling assays with relaxed and closed-circular DNA, recombinant 6b (or human NAP-1 [hNAP-1]) that had been purified from E. coli, and core histones prepared from HeLa cells.
Our observations indicated that 6b had histone chaperone–like activity in vitro but that the activity of 6b was lower than that of hNAP-1 in our assay system.
As shown in Figure 5C, the mutant derivatives of AK6bΔA and AK6bΔC, which lacked tumorigenic activity (Figure 1B), had no histone chaperone–like activity.
In the AK6bΔA sequence (the 564-bp sequence), the 63-bp sequence corresponding to the entire acidic region of 6b (amino acid residues 164 to 184) was deleted from the 6b coding sequence (the 627-bp sequence corresponding to 208–amino acid residues plus the termination codon).
Protein: DP02670 (UniProt P15848)
Region: residues 406	to 422
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Although there is up to 20% of the mature form of the protein in the crystals, the invisibility of this loop is probably due to its flexibility in both the precursor and mature forms of the enzyme, since the loop would be visible if it were ordered only in the precursor form.
In the crystal structure of 4-S, the loop from residues 407 to 422, which is anchored at one end by a disulfide bridge (Cys405– Cys447) and terminates at one of the cleavage sites, is not readily visible in the electron density.
Cross-references: PDB:1FSU
Protein: DP02671 (UniProt P38111)
Region: residues 1	to 235
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The Mec1 N terminus is highly flexible, with more than 200 amino acids (residues 1 to 235) invisible in the structure.
Cross-references: PDB:5X6O
Protein: DP02671 (UniProt P38111)
Region: residues 33	to 43
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron microscopy evidence of the Mec1-Ddc2 in complex with AMP-PNP shows this region lacks electron density, indicating it is disordered.
Cross-references: EMDB:11055
PDB:6Z3A
Protein: DP02671 (UniProt P38111)
Region: residues 1	to 32
Annotation: disorder to order (Structural transition)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron microscopy evidence of the Mec1-Ddc2 shows this region is ordered when interacting with AMP-PNP.
Cross-references: EMDB:11055
PDB:6Z3A
Protein: DP02671 (UniProt P38111)
Region: residues 44	to 235
Annotation: disorder to order (Structural transition)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron microscopy evidence of the Mec1-Ddc2 shows this region is ordered when interacting with AMP-PNP.
Cross-references: EMDB:11055
PDB:6Z3A
Protein: DP02671 (UniProt P38111)
Region: residues 1991	to 2003
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron microscopy evidence of the Mec1-Ddc2 in complex with AMP-PNP shows this region lacks electron density, indicating it is disordered.
Cross-references: EMDB:11055
PDB:6Z3A
Protein: DP02672 (UniProt O35484)
Region: residues 436	to 448
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The structure of AzI has several disordered regions. These include the first seven residues at the N terminus, the last 13 residues at the C terminus, and three disordered loops: amino acids 160–167, which connect β7 to α7; 294–310, connecting β11 to β12; and 330–334 between η3 to β13.
Cross-references: PDB:3BTN
Protein: DP02672 (UniProt O35484)
Region: residues 294	to 310
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The structure of AzI has several disordered regions. These include the first seven residues at the N terminus, the last 13 residues at the C terminus, and three disordered loops: amino acids 160–167, which connect β7 to α7; 294–310, connecting β11 to β12; and 330–334 between η3 to β13.
Cross-references: PDB:3BTN
Protein: DP02673 (UniProt P11926)
Region: residues 422	to 461
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The following residues lacked discernible electron density: 1–18, 31–36, 161–163, 303–308, 345–347, 393–394, and 422–461 in ODC and 220–228 in Az95–2281.
X-ray crystallography failed to provide structural information about the ODC C-tail because this region is disordered in the structures of both the ODC–Az95–2281 heterodimer and the ODC homodimers
Cross-references: PDB:4ZGY
Protein: DP02673 (UniProt P11926)
Region: residues 1	to 18
Annotation: order to disorder (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
This N-terminal segment of ODC (residues 1∼16) is hereafter referred to as the N-latch (Fig. S4 and Fig. 1A), whose conformation is locked in the ODC homodimer by binding across the barrel and sheet domains to mask a prospective proteasome-interacting surface. Az1 binding causes both significant repositioning of the two domains of ODC and rearrangement of the interface contacts (Fig. 2 B and C), which disrupt their interactions with the N-latch and lead to its displacement.
Intriguingly, in ODC–Az95–2281, the fragment becomes fully exposed and thus appears to be suitable for mediating proteasome association due to the disruption of the homodimer interface and an Az1-induced structural transition of the ODC N terminus, which becomes disordered and invisible in the electron density map upon Az1 binding
The N-terminal fragment (residues 1–16, enclosed by black box), which undergoes an order-to-disorder transition upon Az1 binding, is referred to as the N-latch.
Cross-references: PDB:4ZGY
Protein: DP02673 (UniProt P11926)
Region: residues 1	to 18
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
MALDI-TOF mass spectrometry and N-terminal sequencing analysis using an ODC protein sample retrieved from dissolved ODC–Az95–2281 crystals both show the intactness of the ODC N terminus (Fig. S3), providing convincing evidence that the exposure of this presumably proteasome-interacting surface of ODC is caused by an Az1-induced order-to-disorder transition of the ODC N-terminal segment (Fig. 2), rather than by an experimental artifact that resulted from nonspecific proteolysis during sample preparation and crystallization.
Intriguingly, in ODC–Az95–2281, the fragment becomes fully exposed and thus appears to be suitable for mediating proteasome association due to the disruption of the homodimer interface and an Az1-induced structural transition of the ODC N terminus, which becomes disordered and invisible in the electron density map upon Az1 binding
The following residues lacked discernible electron density: 1–18, 31–36, 161–163, 303–308, 345–347, 393–394, and 422–461 in ODC and 220–228 in Az95–2281.
Cross-references: PDB:4ZGY
Protein: DP02673 (UniProt P11926)
Region: residues 422	to 461
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Comparing the spectra of the full-length and truncated homodimers showed that the ODC C-tail is indeed unstructured, being highly flexible and solvent exposed, which gives rise to well-resolved NMR peaks. Moreover, the signals that correspond to the ODC C-tail remained unchanged in the presence of Az95–2281 (Fig. 3B), suggesting that heterodimerization most likely has no effect on the properties of this region.
Protein: DP02674 (UniProt P54368)
Region: residues 110	to 125
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The following residues were missing in the structure: 1–9, 161–167, 294–310, 342–346, and 433–448 in AzIN and 110–125 and 220–228 in Az1 110–228. 
Cross-references: PDB:4ZGZ
Protein: DP02674 (UniProt P54368)
Region: residues 69	to 92
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB of the crystal structure of ODC-PLP-AZ1 ternary complex shows this region lacks electron density, indicating it is disordered.
Protein: DP02675 (UniProt O14977)
Region: residues 294	to 310
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The following residues were missing in the structure: 1–9, 161–167, 294–310, 342–346, and 433–448 in AzIN and 110–125 and 220–228 in Az1 110–228.
Cross-references: PDB:4ZGZ
Protein: DP02675 (UniProt O14977)
Region: residues 433	to 448
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The following residues were missing in the structure: 1–9, 161–167, 294–310, 342–346, and 433–448 in AzIN and 110–125 and 220–228 in Az1 110–228.
Cross-references: PDB:4ZGZ
Protein: DP02676 (UniProt Q9HD36)
Region: residues 107	to 121
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Bcl-B is distinguished from other Bcl-2 family members through an insertion of an unstructured loop between helices α5 and α6.
Residues 107–121 are absent from the electron density for Bcl-B, indicating their flexibility.
A point of similarity between Bcl-B and Boo, which differentiates them both from other Bcl-2 proteins, is the presence of the unstructured α5–α6 loop.
Clear and continuous electron density was obtained for residues 2–106, and 122–164 of Bcl-B and 53–76 of Bim, whereas the residues constituting the α5–α6 loop (residues 107–121) lack clear electron density and were presumed disordered.
Cross-references: PDB:4B4S
Protein: DP02678 (UniProt O75936)
Region: residues 188	to 198
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The model was built for all residues except disordered loop regions, which include residues 188–198, 223–227, 351–359 and two C-terminal residues.
Cross-references: PDB:3N6W
Protein: DP02679 (UniProt Q8R464)
Region: residues 25	to 120
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The Ig1 domain of one mNecl-4 ectodomain (chain C) interacts with mNecl-1 whereas the electron-density of the Ig1 domain of the other mNecl-4 ectodomain (chain A) was essentially missing, indicating that this domain is highly flexible, likely due to the lack of contacts with other molecules in the crystal.
Cross-references: PDB:5ZO2
Protein: DP02680 (UniProt P23280)
Region: residues 21	to 31
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model includes aa 32-279, while aa 21-31 are disordered.
Cross-references: PDB:3FE4
Protein: DP02681 (UniProt B8ZXI1)
Region: residues 292	to 326
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In both polypeptide chains, an expanded segment comprising Cys292–Gln326 obviously is disordered, as no corresponding electron density is visible in the map.
A short turn (Thr295–Gly298) connecting strands βG and βH in bacterial TGT is replaced by an extended putative loop comprising 45 residues (Thr287–Phe331) in QTRT2.
Loop βGβH of QTRT2
Cross-references: PDB:6FV5
Protein: DP02681 (UniProt B8ZXI1)
Region: residues 292	to 326
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In both polypeptide chains, an expanded segment comprising Cys292–Gln326 obviously is disordered, as no corresponding electron density is visible in the map.
A short turn (Thr295–Gly298) connecting strands βG and βH in bacterial TGT is replaced by an extended putative loop comprising 45 residues (Thr287–Phe331) in QTRT2.
Loop βGβH of QTRT2
Cross-references: PDB:6FV5
Protein: DP02682 (UniProt P13797)
Region: residues 1	to 20
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final structure contains 247 residues, with the N-terminal 20 and eight residues in a mobile loop not visible, and 20 water molecules.
Cross-references: PDB:1AOA
Protein: DP02683 (UniProt Q9DBG5)
Region: residues 191	to 205
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 191–205, 289–320, and 432–437 could not be located in the electron density and are presumed disordered.
Cross-references: PDB:1SZI
Protein: DP02683 (UniProt Q9DBG5)
Region: residues 289	to 320
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 191–205, 289–320, and 432–437 could not be located in the electron density and are presumed disordered.
Cross-references: PDB:1SZI
Protein: DP02684 (UniProt P53816)
Region: residues 40	to 57
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 1–5, 40–57, and 126–140 were not modeled because of the weak or absent electron density of these regions.
Region 40-57 corresponds to a disordered loop between β3 and β4
Cross-references: PDB:4DOT
Protein: DP02684 (UniProt P53816)
Region: residues 40	to 57
Annotation: lipid binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 1–5, 40–57, and 126–140 were not modeled because of the weak or absent electron density of these regions.
A region that contributes to the HRASLS2 and HRASLS3 membrane interaction is the 40–57-amino acid segment between β3 and β4.
Thus, the reason for the disorder observed in this particular region could stem from the lack of a proper interfacial environment in the protein crystal, as lipid membrane interactions have been shown to stabilize amphiphilic helices
Cross-references: PDB:4DOT
Protein: DP02684 (UniProt P53816)
Region: residues 40	to 57
Annotation: localization (Biological process)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
A region that contributes to the HRASLS2 and HRASLS3 membrane interaction is the 40–57-amino acid segment between β3 and β4
This in turn suggested an amphiphilic helix with a hydrophobic interface mainly composed of Val-50, Met-51, and Leu-54 in HRASLS3 and Val-50, Leu-51, and Leu-54 in HRASLS2 that could interact with the nonpolar core of a bilayer
The authors suggest that interaction of this region with a lipid bilayer could promote its re-folding as documented for many other amphiphilic helices, although they don't test this hypothesis
Cross-references: PDB:4DOT
Protein: DP02685 (UniProt P40999)
Region: residues 84	to 95
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This loop is presumably unstructured in solution as the electron density for the corresponding amino acids was only observed for one of the four Dnmt2 molecules in the asymmetric unit, and this loop adopted a defined conformation due to formation of crystal contacts with another Dnmt2 molecule in the crystal lattice.
Cross-references: PDB:6FDF
Protein: DP02686 (UniProt Q6XHB2)
Region: residues 1180	to 1193
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Because of its flexibility, the activation loop is not visible in the structure of dephosphorylated Roco4, and in the active form only the main chain can be traced.
Cross-references: PDB:4F0G
Protein: DP02686 (UniProt Q6XHB2)
Region: residues 1180	to 1193
Annotation: phosphorylation display site (Disorder function)
Evidence: enzymatic activity assay evidence used in manual assertion
Supporting statements:
Because of its flexibility, the activation loop is not visible in the structure of dephosphorylated Roco4, and in the active form only the main chain can be traced.
Phosphorylation of serine and threonine residues in kinase-activation loops is important for regulating kinase activity in many protein kinases (22–25). Because the Roco4 kinase becomes autophosphorylated during kinase assays, it is technically difficult to measure the difference in kinase activity in the phosphorylated and dephosphorylated protein. In autophosphorylation assays Roco4 incorporates maximally 2.04 ± 0.33 mol (n = 5) of phosphate per mole of protein. Roco4 kinase contains four putative phosphorylation sites in the activation loop: S1181, S1184, S1187, and S1189
In many kinases, the activation loop is a highly flexible element and contains the primary activity-related phosphorylation sites. In the unphosphorylated, inactive state, this loop often is disordered, but upon phosphorylation it reorients into an ordered, active conformation
Cross-references: PDB:4F0G
Protein: DP02687 (UniProt P24005)
Region: residues 257	to 269
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 1–24 and 257–269 could not be built into the final refined model owing to a lack of electron density, implying that the extreme N-terminal region and the loop connecting α11 and α12 are highly flexible.
Although localised in the C-terminal actin-binding domain (C-domain; residues 181–295), this disordered region is not directly involved in the binding of actin since the actin-binding sites are at amino acids 1–123 (ABS1), 193–254 (ABS2) and 279–295 (ABS3)
Cross-references: PDB:4X3N
Protein: DP02687 (UniProt P24005)
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:
Residues 1–24 and 257–269 could not be built into the final refined model owing to a lack of electron density, implying that the extreme N-terminal region and the loop connecting α11 and α12 are highly flexible.
Cross-references: PDB:4X3N
Protein: DP02688 (UniProt O96759)
Region: residues 543	to 562
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Another disordered loop is close to the C terminus between helices α17 and α18 (residues 543–562). We will refer to it as the “HHH loop” (Figure 2B) because it contains three well-conserved histidines that have a role in substrate binding and/or activity
Inspection of the B factor values of the helix residues reveals a steady increase from the N terminus to the C terminus, the average B factor being 20–30 Å2 higher on the C-terminal helical end. This observation is consistent with the idea that the C-terminal residues of the gating helix can be quite flexible, as suggested by the fact that the helix adopts different conformations in the various protein chains.
Cross-references: PDB:2UUV
PDB:2UUU
Protein: DP02688 (UniProt O96759)
Region: residues 543	to 562
Annotation: entropic chain (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Another disordered loop is close to the C terminus between helices α17 and α18 (residues 543–562). We will refer to it as the “HHH loop” (Figure 2B) because it contains three well-conserved histidines that have a role in substrate binding and/or activity
Access to the tunnel is controlled by a flexible loop and a gating helix at the protein-membrane interface.
The tunnel is accessible from the flavin si face as a consequence of HHH loop disorder
The negatively charged phosphate moiety of the acyl-DHAP substrate might interact with the histidine cluster so that substrate binding might trigger closure of the HHH loop, shielding the active site from solvent.
Cross-references: PDB:2UUV
PDB:2UUU