LiteFold/DisProt huggingface dataset:
Protein: DP02614 (UniProt Q3MIT2)
Region: residues 234	to 243
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The location of the The model also places the tRNA acceptor stem next to a predominantly basic loop, Phe234–Val243, which is disordered in our structure. loop 234–243 is marked by an arrow
The model also places the tRNA acceptor stem next to a predominantly basic loop, Phe234–Val243, which is disordered in our structure. This loop may become ordered upon RNA binding to provide further stabilizing interactions, clamping the RNA substrate.
The final model has one molecule in the asymmetric unit with residues Glu55-Glu62, Leu76–Leu106 and Phe234–Val243 disordered in our crystals
Cross-references: PDB:2V9K
Protein: DP02614 (UniProt Q3MIT2)
Region: residues 55	to 106
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues Glu55–Leu106 connecting α3 and α4 are disordered in our structure. A metal bound in between helix α2 and the loop preceding helix α4 is identified as zinc from a fluorescence scan of the crystal.
Cross-references: PDB:2V9K
Protein: DP02615 (UniProt O75817)
Region: residues 1	to 28
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model of Rpp20/Rpp25 (R/Rfree = 0.20/0.24) was obtained from data to 2.25 Å and, as a result of disordered regions in both the N- and C-termini and between the β3 and β4 antiparallel beta strands, consisted of residues 29 to 59, 63 to 114, and 119 to 140 of Rpp20 and residues 22 to 109 and 125 to 157 of Rpp25
Since the N- and C-terminal regions of both Rpp20 and Rpp25 were disordered in the crystals and our initial datasets were limited in resolution to approximately 3.0 Å, it was difficult to establish the correct amino acid register of the protein models
Cross-references: PDB:6CWX
Protein: DP02616 (UniProt Q9BUL9)
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:
The final model of Rpp20/Rpp25 (R/Rfree = 0.20/0.24) was obtained from data to 2.25 Å and, as a result of disordered regions in both the N- and C-termini and between the β3 and β4 antiparallel beta strands, consisted of residues 29 to 59, 63 to 114, and 119 to 140 of Rpp20 and residues 22 to 109 and 125 to 157 of Rpp25
Since the N- and C-terminal regions of both Rpp20 and Rpp25 were disordered in the crystals and our initial datasets were limited in resolution to approximately 3.0 Å, it was difficult to establish the correct amino acid register of the protein models.
Cross-references: PDB:6CWX
Protein: DP02616 (UniProt Q9BUL9)
Region: residues 158	to 199
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model of Rpp20/Rpp25 (R/Rfree = 0.20/0.24) was obtained from data to 2.25 Å and, as a result of disordered regions in both the N- and C-termini and between the β3 and β4 antiparallel beta strands, consisted of residues 29 to 59, 63 to 114, and 119 to 140 of Rpp20 and residues 22 to 109 and 125 to 157 of Rpp25
Since the N- and C-terminal regions of both Rpp20 and Rpp25 were disordered in the crystals and our initial datasets were limited in resolution to approximately 3.0 Å, it was difficult to establish the correct amino acid register of the protein models.
Cross-references: PDB:6CWX
Protein: DP02617 (UniProt P21575)
Region: residues 497	to 517
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Linkers connecting the MD to the PH and the PH to the GED are disordered, indicating a flexibly tethered PH
Linker connecting MD to PH
Cross-references: PDB:3ZVR
Protein: DP02617 (UniProt P21575)
Region: residues 497	to 517
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Linkers connecting the MD to the PH and the PH to the GED are disordered, indicating a flexibly tethered PH
Linker connecting MD to PH
Cross-references: PDB:3ZVR
Protein: DP02617 (UniProt P21575)
Region: residues 629	to 652
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Linkers connecting the MD to the PH and the PH to the GED are disordered, indicating a flexibly tethered PH
Linker connecting PH to GED
Cross-references: PDB:3ZVR
Protein: DP02617 (UniProt P21575)
Region: residues 629	to 652
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Linkers connecting the MD to the PH and the PH to the GED are disordered, indicating a flexibly tethered PH
Linker connecting PH to GED
Cross-references: PDB:3ZVR
Protein: DP02619 (UniProt Q0WYX8)
Region: residues 736	to 920
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Seven domains (Ig1-6 to FnIII7) could be unequivocally resolved in the electron density maps; however, the C-terminal MAM8 domain was not visible and most likely highly mobile and accommodated in the solvent channels of the crystal.
The MAM8 domain was not visible in the electron density maps, probably due to a flexible FnIII7-MAM8 linker.
Cross-references: PDB:5OJ2
PDB:5OJ6
Protein: DP02620 (UniProt Q14194)
Region: residues 1	to 14
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
As no electron density was detectable for residues 1–14 and 497–572 they were excluded from the final model.
Cross-references: PDB:4B3Z
Protein: DP02620 (UniProt Q14194)
Region: residues 497	to 572
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
As no electron density was detectable for residues 1–14 and 497–572 they were excluded from the final model.
Cross-references: PDB:4B3Z
Protein: DP02620 (UniProt Q14194)
Region: residues 497	to 572
Annotation: phosphorylation display site (Disorder function)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
Analysis of the oligomerization and structural states after the deletion of residues 472–572 by thrombin in vitro revealed discernible differences which, in addition to protein phosphorylation or dephosphorylation events, might be crucial to regulate the function of CRMP and its interaction with other signalling proteins.
Collapsin response mediator proteins (CRMPs) are a family of cytosolic phosphoproteins that were originally investigated as signalling mediators of semaphorin 3A
Several phosphorylation sites are localized in the C-terminal disordered region of CRMP, i.e. a phosphotyrosine at residue 504, a phosphothreonine at residue 509 and phosphoserines at residues 521, 522, 537, 540 and 542 (PTM-sites position as reported in UniProt).
Cross-references: PDB:4B3Z
Protein: DP02621 (UniProt P97427)
Region: residues 491	to 525
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
To characterize the bases of CRMP action, we determined the X‐ray structure of murine CRMP1. Limited proteolysis of CRMP1 (residues 8–572) demonstrated that the C‐terminal segment (approximately 75 amino acids) is proteolytically susceptible (data not shown).
Electron density was visible for residues 15–490, consistent with the proteolysis results described above.
Cross-references: PDB:1KCX
Protein: DP02621 (UniProt P97427)
Region: residues 491	to 525
Annotation: phosphorylation display site (Disorder function)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
Collapsin response mediator proteins (CRMPs) are cytosolic phosphoproteins involved in neuronal differentiation and axonal guidance.
Phosphorylation sites are localized in the ID region
Cross-references: PDB:1KCX
Protein: DP02622 (UniProt Q15113)
Region: residues 189	to 200
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The CPIII-Long:C1C2 structure is isomorphous with the CPIII-His:C1C2 structure, but nearly half of CUB2 could not be modeled due to disorder (missing residues: 133–144, 164–175, 195–208, 217–227).
Region boundaries of the disordered region within CUB2 according to the canonical sequence in UniProt
Cross-references: PDB:6FZW
Protein: DP02622 (UniProt Q15113)
Region: residues 220	to 233
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The CPIII-Long:C1C2 structure is isomorphous with the CPIII-His:C1C2 structure, but nearly half of CUB2 could not be modeled due to disorder (missing residues: 133–144, 164–175, 195–208, 217–227).
Region boundaries of the disordered region within CUB2 according to the canonical sequence in UniProt
Cross-references: PDB:6FZW
Protein: DP02622 (UniProt Q15113)
Region: residues 241	to 252
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The CPIII-Long:C1C2 structure is isomorphous with the CPIII-His:C1C2 structure, but nearly half of CUB2 could not be modeled due to disorder (missing residues: 133–144, 164–175, 195–208, 217–227).
Region boundaries of the disordered region within CUB2 according to the canonical sequence in UniProt
Cross-references: PDB:6FZW
Protein: DP02622 (UniProt Q15113)
Region: residues 151	to 169
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
When compared with the relatively elongated low-resolution structure of full-length PCPE-1 in solution (Bernocco et al., 2003, Kronenberg et al., 2009), the ability of CUB1 and CUB2 to interact in this way in the complex confirms that there is considerable flexibility in the inter-domain linker.
Inter-domain linker connecting CUB1 and CUB2
Cross-references: PDB:6FZW
Protein: DP02622 (UniProt Q15113)
Region: residues 151	to 165
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
When compared with the relatively elongated low-resolution structure of full-length PCPE-1 in solution (Bernocco et al., 2003, Kronenberg et al., 2009), the ability of CUB1 and CUB2 to interact in this way in the complex confirms that there is considerable flexibility in the inter-domain linker.
Inter-domain linker connecting CUB1 and CUB2
Cross-references: PDB:6FZW
Protein: DP02622 (UniProt Q15113)
Region: residues 269	to 278
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The CPIII-Long:C1C2 structure is isomorphous with the CPIII-His:C1C2 structure, but nearly half of CUB2 could not be modeled due to disorder (missing residues: 133–144, 164–175, 195–208, 217–227).
Region boundaries of the disordered region within CUB2 according to the canonical sequence in UniProt.
Cross-references: PDB:6FZW
Protein: DP02623 (UniProt P42003)
Region: residues 215	to 256
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Unfortunately,  the  linker  region  (215—256)  was  flexible  and  disordered  in  the  present  Mad  structure,  indicating  that  there  is  no  observable  contact  between  the  linker  and  MH2  domain.
Flexible linker connecting domains MH1 and MH2
Cross-references: PDB:3GMJ
Protein: DP02623 (UniProt P42003)
Region: residues 215	to 256
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Unfortunately,  the  linker  region  (215—256)  was  flexible  and  disordered  in  the  present  Mad  structure,  indicating  that  there  is  no  observable  contact  between  the  linker  and  MH2  domain.
Flexible linker connecting domains MH1 and MH2
Cross-references: PDB:3GMJ
Protein: DP02624 (UniProt P04775)
Region: residues 1474	to 1486
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Although the termini are mobile and flexible with negative hNOE values, residues in the central portion of the inactivation gate peptide have positive hNOEs indicative of stable structure.
The glycine- and proline-rich regions flanking the folded core are unstructured in both peptide constructs, consistent with their proposed role as hinges in the intact channel
The structured subdomain contains residues functionally implicated in mediating and regulating inactivation and is flanked by regions proposed to serve as hinge regions for the inactivation gate.
The NMR solution structure of the isolated inactivation gate reveals a stably folded core comprised of an α-helix capped by an N-terminal turn, supporting a model in which the tightly folded core containing the latch motif pivots on a more flexible hinge region to occlude the pore during inactivation.
The stably folded core (1487 - 1506) is flanked by N-terminal (1474-1486) and C-terminal (1507-1526) disordered regions that occlude the pore and serve as hinge regions for the inactivation gate
Cross-references: PDB:1BYY
Protein: DP02624 (UniProt P04775)
Region: residues 1474	to 1486
Annotation: entropic chain (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Although the termini are mobile and flexible with negative hNOE values, residues in the central portion of the inactivation gate peptide have positive hNOEs indicative of stable structure.
The glycine- and proline-rich regions flanking the folded core are unstructured in both peptide constructs, consistent with their proposed role as hinges in the intact channel
The structured subdomain contains residues functionally implicated in mediating and regulating inactivation and is flanked by regions proposed to serve as hinge regions for the inactivation gate.
The NMR solution structure of the isolated inactivation gate reveals a stably folded core comprised of an α-helix capped by an N-terminal turn, supporting a model in which the tightly folded core containing the latch motif pivots on a more flexible hinge region to occlude the pore during inactivation.
The stably folded core (1487 - 1506) is flanked by N-terminal (1474-1486) and C-terminal (1507-1526) disordered regions that occlude the pore and serve as hinge regions for the inactivation gate
Cross-references: PDB:1BYY
Protein: DP02624 (UniProt P04775)
Region: residues 1507	to 1526
Annotation: entropic chain (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Although the termini are mobile and flexible with negative hNOE values, residues in the central portion of the inactivation gate peptide have positive hNOEs indicative of stable structure.
The glycine- and proline-rich regions flanking the folded core are unstructured in both peptide constructs, consistent with their proposed role as hinges in the intact channel
The structured subdomain contains residues functionally implicated in mediating and regulating inactivation and is flanked by regions proposed to serve as hinge regions for the inactivation gate.
The stably folded core (1487 - 1506) is flanked by N-terminal (1474-1486) and C-terminal (1507-1526) disordered regions that occlude the pore and serve as hinge regions for the inactivation gate
Cross-references: PDB:1BYY
Protein: DP02624 (UniProt P04775)
Region: residues 1507	to 1526
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Although the termini are mobile and flexible with negative hNOE values, residues in the central portion of the inactivation gate peptide have positive hNOEs indicative of stable structure.
The glycine- and proline-rich regions flanking the folded core are unstructured in both peptide constructs, consistent with their proposed role as hinges in the intact channel
The structured subdomain contains residues functionally implicated in mediating and regulating inactivation and is flanked by regions proposed to serve as hinge regions for the inactivation gate.
The stably folded core (1487 - 1506) is flanked by N-terminal (1474-1486) and C-terminal (1507-1526) disordered regions that occlude the pore and serve as hinge regions for the inactivation gate
Cross-references: PDB:1BYY
Protein: DP02625 (UniProt Q920Q2)
Region: residues 1135	to 1152
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
With the exception of disordered residues at the N terminus, the mRev1 CTD is well structured, with mean pairwise r.m.s.d. of 0.47 and 0.94 Å for the backbone and heavy atoms, respectively
Cross-references: BMRB:18433
PDB:2LSJ
Protein: DP02626 (UniProt Q9QUG2)
Region: residues 546	to 616
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The mPol κ RIR(546–616) displays a typical 1H-15N HSQC spectrum of a disordered peptide, with amide resonances showing a narrow chemical shift distribution.
Cross-references: PDB:2LSJ
Protein: DP02626 (UniProt Q9QUG2)
Region: residues 560	to 582
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The mPol κ RIR(546–616) displays a typical 1H-15N HSQC spectrum of a disordered peptide, with amide resonances showing a narrow chemical shift distribution.
By analyzing mPol κ RIR amide resonances that experience substantial perturbations upon binding to the mRev1 CTD, we have identified a 23-residue RIR peptide of mPol κ(560–582) that not only binds to the mRev1 CTD tightly but also causes identical resonance perturbations for the mRev1 CTD as the longer peptide. This 23-residue peptide was subsequently used to investigate the mRev1 CTD-Pol κ RIR interaction.
Cross-references: PDB:2LSJ
Protein: DP02626 (UniProt Q9QUG2)
Region: residues 566	to 575
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The mPol κ RIR(546–616) displays a typical 1H-15N HSQC spectrum of a disordered peptide, with amide resonances showing a narrow chemical shift distribution.
The binding of the mRev1 CTD similarly induces folding of the disordered Pol κ RIR into a three-turn α-helix, starting from Phe566 and ending at Ile575
Cross-references: PDB:2LSJ
Protein: DP02626 (UniProt Q9QUG2)
Region: residues 560	to 582
Annotation: molecular adaptor activity (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The eukaryotic Y-family polymerase Rev1 is an essential scaffolding protein in translesion synthesis. Its C-terminal domain (CTD), which interacts with translesion polymerase ζ through the Rev7 subunit and with polymerases κ, ι, and η in vertebrates through the Rev1-interacting region (RIR), is absolutely required for function.
Our combined structural and biochemical studies reveal two distinct surfaces of the Rev1 CTD that separately mediate the assembly of extension and insertion translesion polymerase complexes and provide a molecular framework for developing novel cancer therapeutics to inhibit translesion synthesis.
Protein: DP02627 (UniProt Q8TEP8)
Region: residues 201	to 214
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-termini and C-termini of both Cep192 -58mer (201–214 and 242–258) and Cep152-60mer (1–15 and 47–60) were disordered, suggesting that these regions are highly flexible upon binding to CPB.
Cep192-58mer corresponds to Cep192 (201–258) fragment
Cross-references: PDB:4N7Z
Protein: DP02627 (UniProt Q8TEP8)
Region: residues 242	to 258
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-termini and C-termini of both Cep192 -58mer (201–214 and 242–258) and Cep152-60mer (1–15 and 47–60) were disordered, suggesting that these regions are highly flexible upon binding to CPB.
Cep192-58mer corresponds to Cep192 (201–258) fragment
Cross-references: PDB:4N7Z
Protein: DP02627 (UniProt Q8TEP8)
Region: residues 242	to 258
Annotation: order to disorder (Structural transition)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-termini and C-termini of both Cep192 -58mer (201–214 and 242–258) and Cep152-60mer (1–15 and 47–60) were disordered, suggesting that these regions are highly flexible upon binding to CPB.
Cep192-58mer corresponds to Cep192 (201–258) fragment
Cross-references: PDB:4N7Z
Protein: DP02627 (UniProt Q8TEP8)
Region: residues 201	to 214
Annotation: order to disorder (Structural transition)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-termini and C-termini of both Cep192 -58mer (201–214 and 242–258) and Cep152-60mer (1–15 and 47–60) were disordered, suggesting that these regions are highly flexible upon binding to CPB.
Cep192-58mer corresponds to Cep192 (201–258) fragment
Cross-references: PDB:4N7Z
Protein: DP02628 (UniProt O94986)
Region: residues 1	to 15
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-termini and C-termini of both Cep192 -58mer (201–214 and 242–258) and Cep152-60mer (1–15 and 47–60) were disordered, suggesting that these regions are highly flexible upon binding to CPB.
Cep152-60mer corresponds to Cep152 (1–60) fragment
Cross-references: PDB:4N7V
Protein: DP02628 (UniProt O94986)
Region: residues 47	to 60
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-termini and C-termini of both Cep192 -58mer (201–214 and 242–258) and Cep152-60mer (1–15 and 47–60) were disordered, suggesting that these regions are highly flexible upon binding to CPB.
Cep152-60mer corresponds to Cep152 (1–60) fragment
Cross-references: PDB:4N7V