LiteFold/DisProt huggingface dataset:
Protein: DP02408 (UniProt Q9P2K3-3)
Region: residues 1	to 272
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model consists of residues 171 to 836 of LSD1/KDM1A, a FAD molecule, and residues 273 to 405 of CoREST3
Cross-references: PDB:4CZZ
Protein: DP02408 (UniProt Q9P2K3-3)
Region: residues 406	to 553
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model consists of residues 171 to 836 of LSD1/KDM1A, a FAD molecule, and residues 273 to 405 of CoREST3
Cross-references: PDB:4CZZ
Protein: DP02409 (UniProt Q9BTT0)
Region: residues 186	to 213
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Anp32e residues 186-213 and 225-232 were not observable in the structure because of lack of electron density
We determined the crystal structure of the Anp32e chaperone domain (186-232) in complex with the H2A.Z-H2B dimer. In this structure, the region containing Anp32e residues 214-224, which is absent in other Anp32 family proteins, specifically interacts with the extended H2A.Z αC helix, which exhibits an unexpected conformational change.
Cross-references: PDB:4NFT
Protein: DP02409 (UniProt Q9BTT0)
Region: residues 214	to 224
Annotation: disorder to order (Structural transition)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
We determined the crystal structure of the Anp32e chaperone domain (186-232) in complex with the H2A.Z-H2B dimer. In this structure, the region containing Anp32e residues 214-224, which is absent in other Anp32 family proteins, specifically interacts with the extended H2A.Z αC helix, which exhibits an unexpected conformational change.
The overall structure of the Anp32e186-232-lnkH2B-H2A.Z complex. The sequence of the observable part of Anp32e in the structure is 214EEVGLSYLMKE224
Cross-references: PDB:4NFT
Protein: DP02409 (UniProt Q9BTT0)
Region: residues 214	to 224
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
We determined the crystal structure of the Anp32e chaperone domain (186-232) in complex with the H2A.Z-H2B dimer. In this structure, the region containing Anp32e residues 214-224, which is absent in other Anp32 family proteins, specifically interacts with the extended H2A.Z αC helix, which exhibits an unexpected conformational change.
The overall structure of the Anp32e186-232-lnkH2B-H2A.Z complex. The sequence of the observable part of Anp32e in the structure is 214EEVGLSYLMKE224
Cross-references: PDB:4NFT
Protein: DP02409 (UniProt Q9BTT0)
Region: residues 186	to 232
Annotation: protein folding chaperone (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
We determined the crystal structure of the Anp32e chaperone domain (186-232) in complex with the H2A.Z-H2B dimer. 
Cross-references: PDB:4NFT
Protein: DP02410 (UniProt P21952)
Region: residues 319	to 342
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The final model comprises POU specific (POUS) and POU homeodomain (POUHD) but the connecting linker was structurally disordered and could thus not be built.
Cross-references: PDB:2XSD
Protein: DP02410 (UniProt P21952)
Region: residues 319	to 342
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The final model comprises POU specific (POUS) and POU homeodomain (POUHD) but the connecting linker was structurally disordered and could thus not be built.
Cross-references: PDB:2XSD
Protein: DP02411 (UniProt Q08050)
Region: residues 222	to 231
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Neither molecule displays electron density for the first 10 N-terminal residues or the 25–30 C-terminal ones, indicating a degree of disorder in these regions.
Our model consists of: the entire double-stranded DNA molecule; 2 magnesium ions; 163 water molecules; FoxM1 residues 232–321 in the A molecule and residues 235–327 in the B molecule
Cross-references: PDB:3G73
Protein: DP02411 (UniProt Q08050)
Region: residues 327	to 360
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Neither molecule displays electron density for the first 10 N-terminal residues or the 25–30 C-terminal ones, indicating a degree of disorder in these regions.
Our model consists of: the entire double-stranded DNA molecule; 2 magnesium ions; 163 water molecules; FoxM1 residues 232–321 in the A molecule and residues 235–327 in the B molecule
Cross-references: PDB:3G73
Protein: DP02411 (UniProt Q08050)
Region: residues 1	to 114
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
To probe the structures of the NRD and TAD once they are dissociated, we acquired circular dichroism (CD) spectra on isolated human NRD (residues 1–114) and TAD (694-748) domains and compared them to the human homolog of the NRD-TAD fusion construct used for NMR (1-117/694-748; Δ25–50) (Figure 5A and Figure 5—figure supplement 1A). We used the minimal NRD construct for CD analysis, because NMR data suggest the region between 115–203 is disordered (Figure 5—figure supplement 2).
WT NRD alone is already considerably disordered
We observe that while both the FoxM1 NRD and TAD are primarily intrinsically disordered domains, they associate and adopt a structured conformation.
In contrast, the TAD and NRD spectra indicate relatively greater disorder, although they do reflect some secondary structure content.
Protein: DP02411 (UniProt Q08050)
Region: residues 694	to 748
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
To probe the structures of the NRD and TAD once they are dissociated, we acquired circular dichroism (CD) spectra on isolated human NRD (residues 1–114) and TAD (694-748) domains and compared them to the human homolog of the NRD-TAD fusion construct used for NMR (1-117/694-748; Δ25–50) (Figure 5A and Figure 5—figure supplement 1A).
In contrast, the TAD and NRD spectra indicate relatively greater disorder, although they do reflect some secondary structure content.
Protein: DP02411 (UniProt Q08050)
Region: residues 694	to 748
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
We tested three common TAD interaction domains in CBP and found that purified TAZ2 and KIX domains bind the FoxM1 TAD, while TAZ1 does not 
Using sequence conservation we designed a minimal NRD (1-114) and minimal TAD (696-748) and found that they associate with comparable affinity (Kd = 3 ± 2 µM).
Protein: DP02411 (UniProt Q08050)
Region: residues 1	to 114
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
Both the NRD and fusion elute in earlier fractions than expected based on their molecular weights, suggesting larger hydrodynamic radii than the standard globular proteins due to structural disorder.
Protein: DP02411 (UniProt Q08050)
Region: residues 1	to 114
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
 Using sequence conservation we designed a minimal NRD (1-114) and minimal TAD (696-748) and found that they associate with comparable affinity (Kd = 3 ± 2 µM).
Protein: DP02412 (UniProt O88513)
Region: residues 79	to 89
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-terminal ten residues are structured in the tGeminin monomer that binds to tCdt1 but are disordered in the other tGeminin monomer, indicating that this region might undergo induced folding after binding to tCdt1
Here we describe the crystal structure of the mouse geminin–Cdt1 complex using tGeminin (residues 79–157, truncated geminin) and tCdt1 (residues 172–368, truncated Cdt1). The amino-terminal region of a coiled-coil dimer of tGeminin interacts with both N-terminal and carboxy-terminal parts of tCdt1
Cross-references: PDB:2ZXX
Protein: DP02412 (UniProt O88513)
Region: residues 79	to 89
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The N-terminal ten residues are structured in the tGeminin monomer that binds to tCdt1 but are disordered in the other tGeminin monomer, indicating that this region might undergo induced folding after binding to tCdt1
Here we describe the crystal structure of the mouse geminin–Cdt1 complex using tGeminin (residues 79–157, truncated geminin) and tCdt1 (residues 172–368, truncated Cdt1). The amino-terminal region of a coiled-coil dimer of tGeminin interacts with both N-terminal and carboxy-terminal parts of tCdt1
Cross-references: PDB:2ZXX
Protein: DP02412 (UniProt O88513)
Region: residues 79	to 89
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The N-terminal ten residues are structured in the tGeminin monomer that binds to tCdt1 but are disordered in the other tGeminin monomer, indicating that this region might undergo induced folding after binding to tCdt1
Here we describe the crystal structure of the mouse geminin–Cdt1 complex using tGeminin (residues 79–157, truncated geminin) and tCdt1 (residues 172–368, truncated Cdt1). The amino-terminal region of a coiled-coil dimer of tGeminin interacts with both N-terminal and carboxy-terminal parts of tCdt1
The crystal structure, in conjunction with our biochemical data, indicates that the N-terminal region of tGeminin might be required to anchor tCdt1
In the second part of the tGeminin–tCdt1 interface, a surface groove on Cdt1 formed by helix H6 and loop L2 of tCdt1 binds the ten residues in the N-terminal loop of tGemimin monomer (Fig. 2b).
The ten residues immediately N-terminal to the coiled-coil domain form a loop and a short helix. These residues and the N-terminal part of the coiled coil of tGeminin bind to tCdt1.
Cross-references: PDB:2ZXX
Protein: DP02412 (UniProt O88513)
Region: residues 79	to 89
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
Structural basis for inhibition of the replication licensing factor Cdt1 by geminin" Article "The deletion of these ten residues decreased tGeminin's binding affinity to tCdt1 about 15-fold (Supplementary Table 2).
Dissociation constants of Cdt1 to geminin - determined by ITC (Supplementary Table 2) - correspond to 4.4 ± 2.2 nM in the case of tGeminin (geminin79-157) and to 56.2 ± 10.1 nM in the case of geminin89-157 where the first ten residues are deleted, thus indicating a decrease in the binding affinity.
Protein: DP02413 (UniProt P04198)
Region: residues 28	to 60
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 28–60 of N-Myc are not observed in the structure, whereas residues 61–89 are associated with the cleft between the N- and C-lobes of the Aurora-A kinase domain formed by the αB/αC helices, the activation loop, and the αG helix
The section of the AIR that was not resolved in the crystal structure, residues 28–60 of N-Myc, includes the MB0 and MBI regions and is conserved in c-Myc
residues 28–89 of N-Myc as the minimal Aurora-A–interaction region (AIR), which spans MB0 through MBI but does not include MBII or beyond
Other conserved sequence motifs called “Myc boxes” (MB0–IV) serve as docking sites for protein–protein interactions. The Myc transactivation domain (TAD) spans the N-terminal conserved motifs MB0, MBI, and MBII
Cross-references: PDB:5G1X
Protein: DP02414 (UniProt P14653)
Region: residues 187	to 206
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The hexapeptide is joined to the HoxB1 homeodomain by a flexible linker, of which 20 amino acids (residues −17 to +3) are disordered in the ternary complex structure.
20 disordered residues in the HoxB1 linker
This hexapeptide, whose consensus sequence is hydrophobic-Y/F -P-W-M-K/R, is joined to the N-terminal arm of the homeodomain by a linker that varies in length and sequence among different Hox proteins and between different species.
Cross-references: PDB:1B72
Protein: DP02414 (UniProt P14653)
Region: residues 187	to 206
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The hexapeptide is joined to the HoxB1 homeodomain by a flexible linker, of which 20 amino acids (residues −17 to +3) are disordered in the ternary complex structure.
20 disordered residues in the HoxB1 linker
This hexapeptide, whose consensus sequence is hydrophobic-Y/F -P-W-M-K/R, is joined to the N-terminal arm of the homeodomain by a linker that varies in length and sequence among different Hox proteins and between different species.
Cross-references: PDB:1B72
Protein: DP02415 (UniProt P54274)
Region: residues 1	to 10
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Although the hTRF1(1–55) fragment was used in our crystallization and the fragment remained intact in our crystallographic lattice (Supplementary Fig. S1), only hTRF1 residues 11–22 were clearly visible in the electron-density map.
Cross-references: PDB:5HKP
Protein: DP02415 (UniProt P54274)
Region: residues 23	to 55
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Although the hTRF1(1–55) fragment was used in our crystallization and the fragment remained intact in our crystallographic lattice (Supplementary Fig. S1), only hTRF1 residues 11–22 were clearly visible in the electron-density map.
Cross-references: PDB:5HKP
Protein: DP02417 (UniProt P49765)
Region: residues 37	to 46
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
ne of the major conformational changes in VEGF-B10–108 structure is observed in the loop comprising residues 37–46 of VEGF-B10–108
The Cα atoms of Leu39, Met40, and Gly41 are displaced by 5.7 Å, 5.2 Å, and 5.8 Å, respectively. This loop is involved in crystal packing with the constant domain of the Fab molecule. Extensive symmetry-related interactions have stabilised the loop, which was disordered in the native structure of VEGF-B10–108
Despite preservation of the overall structure in the complex, conformational differences in three loop regions 37–46, 61–67, and 84–89 of the VEGF-B10–108 dimer were observed.
Here, we present the structural features of the ‘highly ordered’ interaction of the Fab fragment of this antibody (Fab-2H10) with VEGF-B.
Cross-references: PDB:2VWE
Protein: DP02417 (UniProt P49765)
Region: residues 37	to 46
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
ne of the major conformational changes in VEGF-B10–108 structure is observed in the loop comprising residues 37–46 of VEGF-B10–108
The Cα atoms of Leu39, Met40, and Gly41 are displaced by 5.7 Å, 5.2 Å, and 5.8 Å, respectively. This loop is involved in crystal packing with the constant domain of the Fab molecule. Extensive symmetry-related interactions have stabilised the loop, which was disordered in the native structure of VEGF-B10–108
Despite preservation of the overall structure in the complex, conformational differences in three loop regions 37–46, 61–67, and 84–89 of the VEGF-B10–108 dimer were observed.
Here, we present the structural features of the ‘highly ordered’ interaction of the Fab fragment of this antibody (Fab-2H10) with VEGF-B.
Cross-references: PDB:2VWE
Protein: DP02417 (UniProt P49765)
Region: residues 37	to 46
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
One of the major conformational changes in VEGF-B10–108 structure is observed in the loop comprising residues 37–46 of VEGF-B10–108
The Cα atoms of Leu39, Met40, and Gly41 are displaced by 5.7 Å, 5.2 Å, and 5.8 Å, respectively. This loop is involved in crystal packing with the constant domain of the Fab molecule. Extensive symmetry-related interactions have stabilised the loop, which was disordered in the native structure of VEGF-B10–108
Despite preservation of the overall structure in the complex, conformational differences in three loop regions 37–46, 61–67, and 84–89 of the VEGF-B10–108 dimer were observed.
Here, we present the structural features of the ‘highly ordered’ interaction of the Fab fragment of this antibody (Fab-2H10) with VEGF-B.
Cross-references: PDB:2VWE
Protein: DP02417 (UniProt P49765)
Region: residues 130	to 188
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron density for the first N-terminal residue and the last C-terminal residue could not be observed for both monomers of VEGF-B10–108. Both chains consist of residues 11–107.
Cross-references: PDB:2VWE
Protein: DP02418 (UniProt P35568)
Region: residues 117	to 159
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 117–159 corresponding to the interdomain linker are disordered
No electron density is observed for the interdomain linker region (residues 117–159). Considering the linker composition, this is not surprising; 26 (60%) of the 43 residues are glycine, alanine, and serine. Unlike the PH and PTB domains, whose sequences are well conserved, interdomain linkers of the four IRS proteins vary greatly in length, from 28 to 51 residues, and composition, suggesting that this region of each IRS protein serves similarly as a flexible tether between PH and PTB domains.
Because the linker is disordered, it is not possible to unequivocally establish covalent connections between domains
The final model includes all residues of the PH (12–116) and PTB (160–264) domains and 90 solvent molecules. Residues 117–159 corresponding to the interdomain linker are disordered.
The nonconserved 46-residue linker between the domains is disordered
Cross-references: PDB:1QQG
Protein: DP02418 (UniProt P35568)
Region: residues 117	to 159
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 117–159 corresponding to the interdomain linker are disordered
No electron density is observed for the interdomain linker region (residues 117–159). Considering the linker composition, this is not surprising; 26 (60%) of the 43 residues are glycine, alanine, and serine. Unlike the PH and PTB domains, whose sequences are well conserved, interdomain linkers of the four IRS proteins vary greatly in length, from 28 to 51 residues, and composition, suggesting that this region of each IRS protein serves similarly as a flexible tether between PH and PTB domains.
Because the linker is disordered, it is not possible to unequivocally establish covalent connections between domains
The final model includes all residues of the PH (12–116) and PTB (160–264) domains and 90 solvent molecules. Residues 117–159 corresponding to the interdomain linker are disordered.
The nonconserved 46-residue linker between the domains is disordered
Cross-references: PDB:1QQG
Protein: DP02419 (UniProt Q5SQI0)
Region: residues 26	to 36
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The refined αTAT1/AcCoA structure reveals continuous electron density from amino acid 3 to 195, except for two short unresolved loops (residues 26–36 and 84–91)
Cross-references: PDB:4GS4
Protein: DP02419 (UniProt Q5SQI0)
Region: residues 196	to 236
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The refined αTAT1/AcCoA structure reveals continuous electron density from amino acid 3 to 195, except for two short unresolved loops (residues 26–36 and 84–91)
An expression construct encoding residues 2–236 of human αTAT1 was shown to retain almost 100% of microtubule acetyltransferase activity relative to the full-length protein, and secondary structure prediction algorithms suggested that the C terminus of the protein, residues ∼230–333, were disordered
Although the expression construct used for crystallization contained ∼40 residues C-terminal to the last resolved residue, and confirmed by mass spectrometry to be present in the crystals, this portion of the protein was not observed in the electron density map
Based on this result, we conclude that residues 196–236 are disordered in the crystals.
We found it interesting that residues 196–236 of αTAT1 were disordered in the crystal structure because K233 was reported to be acetylated, suggesting that K233 acetylation does not play a regulatory role for catalysis
Cross-references: PDB:4GS4
Protein: DP02419 (UniProt Q5SQI0)
Region: residues 231	to 235
Annotation: acetylation display site (Disorder function)
Evidence: enzymatic activity assay evidence used in manual assertion
Supporting statements:
An expression construct encoding residues 2–236 of human αTAT1 was shown to retain almost 100% of microtubule acetyltransferase activity relative to the full-length protein, and secondary structure prediction algorithms suggested that the C terminus of the protein, residues ∼230–333, were disordered
We found it interesting that residues 196–236 of αTAT1 were disordered in the crystal structure because K233 was reported to be acetylated, suggesting that K233 acetylation does not play a regulatory role for catalysis, similar to autoacetylation sites in the Rtt109 and MYST histone acetyltransferases (HATs) that are highly ordered in the corresponding crystal structures (15, 21).
Cross-references: PDB:4GS4
Protein: DP02420 (UniProt Q86YV5)
Region: residues 932	to 943
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