LiteFold/DisProt huggingface dataset:
Protein: DP03440 (UniProt P04968)
Region: residues 481	to 496
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The zone of missing residues 481–496 is on the exterior of the domain, in a position where a helix would be expected in order to complete the second α+β plait motif.
The regulatory domain is at the top in magenta and orange. The missing zone (residues 481–496) is indicated by a dotted line. (Secondary structure assignments were made using the program DSSP [24].)
The black spheres show the start and end of the missing zone (residues 481–496) in TD the structure of which may be similar to the rightmost PGD helix.
 The final model lacks residues 1–4 at the N terminus and also lacks residues 481–496. This missing zone in the regulatory domain corresponds to a highly exposed connection between two β strands, where electron-density maps show the presence of the polypeptide but are insufficiently ordered to construct it. The distance between residues 480 and 497 and the extent of the intervening weak density correspond reasonably well with
the number of missing residues, and there is no ambiguity about the topology or fold
Cross-references: PDB:1TDJ
Protein: DP03442 (UniProt P59635)
Region: residues 81	to 94
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Residues 66–84 appear to be unstructured, indicated by decreased heteronuclear 1H-15N-NOE values (Figure 3) and the lack of experimental NOE-derived structural data for this part of the protein.
Both 15N T2 and steady-state 1H-15N NOE values support the hypothesis of an unstructured carboxy-terminal region encompassing residues 66–84 in contrast to the well-folded b-sandwich comprising residues 1–65.
Cross-references: PDB:1YO4
Protein: DP03444 (UniProt Q9UPP1)
Region: residues 101	to 113
Annotation: flexible linker (Disorder function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
To  understand  how  H3K4me3  binding  enhances  demethylase activity, we determined the cocrystal structure of PHF81–447 with an H31–24 peptide containing H3K4me3 and H3K9me2 (Fig. 1e) in the presence of Fe2+ and N-oxalylglycine (the cofactor analog) to form a  catalytically  inert  complex  (Table  1).  The  structure,  determined at a resolution of 2.2 Å, shows that the PHD and jumonji domains act in concert in substrate recognition. The first 11 residues of the H3  peptide  were  nearly  buried  in  a  deep  cleft  between  the  PHD and the jumonji domains with a disordered linker (residues 66–78)  (Fig. 1e).
The IDR characterized in the publication and spanning residues 66-78 corresponds residues 102-114 of the canonical sequence in UniProt, since the authors determined a structure of PHF8 without the first 36 aminoacids. 
Cross-references: PDB:3KV4
Protein: DP03444 (UniProt Q9UPP1)
Region: residues 101	to 113
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The first 11 residues of the H3 peptide were nearly buried in a deep cleft between the PHD and the jumonji domains with a disordered linker (residues 66–78) (Fig. 1e).
Cross-references: PDB:3KV4
Protein: DP03445 (UniProt P0C066)
Region: residues 20	to 29
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
As the MS analysis for the recombinant protein gives the expected mass value (Mr = 38 495 ± 4; predicted mass of Mr = 38 493) for the amino-acid residues 19−259 construct, residues 19−29 are present but are not seen
in the electron density due to disorder (as is also predicted by the DisEMBL server (http://dis.embl.de/).
We noted that the stretch of amino acids 19−29 in the MltC structure is
disordered. 
It is tempting to speculate that the disorder within the residues 19−29 would impart the ability for a rotational motion to MltC to sweep out a large annulus of cleared peptidoglycan per each molecule of enzyme (Figure
4B), which would enable insertion of a large assembly such as that of the flagellum.
(B) Rotational motion of a single membrane bound MltC with its disordered linker (residues 19−29, depicted in light brown) could create a large annulus of cleared peptidoglycan.
The N-terminus, the site of attachment of residues 19−29 and the fatty acyl membrane anchor, which is not seen in the electron density, is indicated by an arrow at 11 o’clock.
Cross-references: PDB:4C5F
Protein: DP03446 (UniProt Q9NR48)
Region: residues 2090	to 2107
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The AWS domain is composed of mostly loops and two short -helices. These loops are bound by two zinc atoms and coordinated by eight conserved cysteines in the AWS domain. The fact that the AWS domain in one of the two molecules of the asymmetric unit is partially disordered and that the temperature factor of the AWS domain is high suggests that the AWS domain is highly flexible.
the IDR characterized in the publication and spanning residues 2082-2103 corresponds to region 2090-2107 of the UniProt canonical ASH1L sequence.
Protein: DP03446 (UniProt Q9NR48)
Region: residues 2268	to 2272
Annotation: methylation display site (Disorder function)
Evidence: methylation assay evidence used in manual assertion
Supporting statements:
We crystallized the Q2265A mutant protein, and preliminary structural analysis of the mutant protein shows that the auto-inhibitory loop is highly disordered. With these mutants, we observed an increased level of HMTase activity for hASH1L, with higher levels of activity observed for Q2265A than for N2197A (Fig. 2D). 
Mutating Asn-2197 or Gln-2265 to alanine (N2197A,Q2265A) increases HMTase activity
The residue, Gln2265 characterized in the publication corresponds to residue, Gln2270 of the UniProt ASH1L canonical sequence
Protein: DP03446 (UniProt Q9NR48)
Region: residues 2263	to 2267
Annotation: methylation display site (Disorder function)
Evidence: methylation assay evidence used in manual assertion
Supporting statements:
Unexpectedly, the F2260A mutant showed no activity toward either the nucleosomal array or the mononucleosome substrates. 
Mutating Asn-2197 or Gln-2265 to alanine (N2197A,Q2265A) increases HMTase activity, whereas F2260A or Q2266A mutations abolish the activity.
The residue, Phe2260 characterized in the publication corresponds to residue, Phe2265 of the UniProt ASH1L canonical sequence
Protein: DP03446 (UniProt Q9NR48)
Region: residues 2269	to 2273
Annotation: methylation display site (Disorder function)
Evidence: methylation assay evidence used in manual assertion
Supporting statements:
In a third mutant, we mutated the Gln-2266 residue to Ala to perturb the interaction of the protein with AdoMet. In this mutant, we were not able to see any HMTase activity, suggesting that the Gln-2266 residue is critical for activity. 
Mutating Asn-2197 or Gln-2265 to alanine (N2197A,Q2265A) increases HMTase activity, whereas F2260A or Q2266A mutations abolish the activity.
The residue, Gln2266 characterized in the publication corresponds to residue, Gln2271 of the UniProt ASH1L canonical sequence
Protein: DP03446 (UniProt Q9NR48)
Region: residues 2263	to 2271
Annotation: self-inhibition (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
We refer to the loop occupying the substrate binding pocket as the “auto-inhibitory loop.” The auto-inhibitory loop is highly flexible, as indicated by its high temperature factor, suggesting that the loop can be repositioned upon substrate binding.
The region characterized in the publication and spanning residues 2258-2266 corresponds to region 2263-2271 of the UniProt canonical ASH1L sequence
Protein: DP03446 (UniProt Q9NR48)
Region: residues 2263	to 2271
Annotation: self-inhibition (Disorder function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The structure reveals the architecture of the core of the AMC HMTase complex and uncovers an allosteric mechanism by which binding of MRG15 to one interface on the SET domain results in the disordering of the AI loop to permit substrate binding on the opposite surface of this domain. 
We find that, in the structure of the  ASH1LSET_MRG15MRG complex, the AI loop is disordered in both molecules in the asymmetric unit of the crystal (Figure 2A). 
(A) The autoinhibitory loop is disordered in the ASH1L_MRG15 (I) complex (left) and partially ordered in the ASH1L_MRG15 (II) complex (right). 
(B) Superimposition of ASH1L alone and the ASH1L_MRG complexes (I and II), showing the structural changes in the autoinhibitory loop and SET-I loop upon MRG15 binding.
(A) H2193 near the autoinhibitory loop is displaced from the loop in ASH1L_MRG15 (form I) where the loop is disordered, and H2193 interacts with the loop in the structures where the loop is ordered (form II and alone). 
Cross-references: PDB:6AGO
Protein: DP03446 (UniProt Q9NR48)
Region: residues 2261	to 2269
Annotation: self-inhibition (Disorder function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The most striking difference between the Mrg15-bound and thefree hAsh1L SET domains occurs at an autoinhibitory loop, whichranges from residues N2257 to K2264 in the post-SET region. It becomes disordered in the hAsh1L-Mrg15 complex (Figure 1B).
The disordered autoinhibitory loop in the hAsh1L-Mrg15 complex indicates that the conformation of this loop is dynamic upon Mrg15 binding, allowing easier access of H3K36 to the active site of hAsh1L for methylation.
The region characterized in the publication and spanning residues 2257-2264 corresponds to region 2261-2269 of the UniProt canonical ASH1L sequence
Cross-references: PDB:6INE
Protein: DP03446 (UniProt Q9NR48)
Region: residues 2261	to 2284
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
We refer to the loop occupying the substrate binding pocket as the “auto-inhibitory loop.” The auto-inhibitory loop is highly flexible, as indicated by its high temperature factor, suggesting that the loop can be repositioned upon substrate binding
Cross-references: PDB:3OPE
Protein: DP03446 (UniProt Q9NR48)
Region: residues 2261	to 2273
Annotation: self-inhibition (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Using X-ray crystallography and nuclear magnetic resonance (NMR), we found that two loops surrounding the active site of ASH1L, the autoinhibitory loop and a loop in the SET-I subdomain, undergo concerted conformational dynamics.
We found that the autoinhibitory loop and the AWS region have the highest B factors, suggesting that these are more mobile regions (Figure 1C). 
The region characterized in the publication and spanning residues 2255-2268 corresponds to region 2261-2273 of the UniProt canonical ASH1L sequence
Cross-references: PDB:4YPU
PDB:4YNM
PDB:4YPA
PDB:4YNP
PDB:4YPE
Protein: DP03446 (UniProt Q9NR48)
Region: residues 2261	to 2273
Annotation: self-inhibition (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Using X-ray crystallography and nuclear magnetic resonance (NMR), we found that two loops surrounding the active site of ASH1L, the autoinhibitory loop and a loop in the SET-I subdomain, undergo concerted conformational dynamics.
This observation strongly suggests that the autoinhibitory and SET-I loops surrounding the active site of ASH1L experience conformational dynamics, in agreement with crystallographic data presented above.
Protein: DP03447 (UniProt Q13177)
Region: residues 1	to 108
Annotation: localization (Biological process)
Evidence: deletion mutation phenotypic evidence used in manual assertion
Supporting statements:
Notably, we also made truncations deleting the kinase domain and variable regions of PAK2 and PAK3, and, similar to what we observed for PAK1, whereas full-length PAK2 and PAK3 do not target to junctions, GFP-PAK2(1–108) and GFP-PAK3(1–109) target very well (Fig. 3D).
Nonetheless, these constructs support the conclusion that the N-terminal and CRIB domain regions of type I PAKs can target to cell–cell boundaries, and the variable region inhibits targeting.
Protein: DP03447 (UniProt Q13177)
Region: residues 71	to 92
Annotation: protein binding (Molecular function)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
Interaction of PAK2(71−92) with sNBD-labeled Cdc42 (21) was followed by changes in extrinsic fluorescence with the addition of varying amounts of the peptide (0−2.5 μM).
The increment in fluorescence is plotted, and the line represents a fit of the data to a simple model for bimolecular association.
Protein: DP03447 (UniProt Q13177)
Region: residues 71	to 92
Annotation: protein binding (Molecular function)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
Proton NMR studies of PAK2(71−92) demonstrate structuring of PAK2(71−92) in the presence of GTP-γS-loaded Cdc42, through the observation of many nonsequential transferred NOEs. Structure calculations based on the observed transferred NOEs show that the central portion of the Cdc42-bound CRIB peptide assumes a loop conformation in which the side chains of consensus residues Phe80, His82, Ile84, His85, and Val86 are brought into proximity.
Protein: DP03447 (UniProt Q13177)
Region: residues 71	to 92
Annotation: disorder to order (Structural transition)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
Proton NMR studies of PAK2(71−92) demonstrate structuring of PAK2(71−92) in the presence of GTP-γS-loaded Cdc42, through the observation of many nonsequential transferred NOEs. Structure calculations based on the observed transferred NOEs show that the central portion of the Cdc42-bound CRIB peptide assumes a loop conformation in which the side chains of consensus residues Phe80, His82, Ile84, His85, and Val86 are brought into proximity. 
 Interestingly, interaction of PAK2(71−92) with GTP-γS-loaded Cdc42 leads to structuring of this peptide, as evidenced by the appearance of many transferred NOEs. Similar NOEs are not observed in the free peptide, and are significantly attenuated in the presence of GDP-bound Cdc42. Although the structure of the entire peptide is not well defined, residues Pro77−Ala90 fold into a unique conformation upon binding to the “active” form of Cdc42. Structure calculations revealed a loop conformation condensed around a hydrophobic cluster comprised of residues Phe80, His82, Ile84, His85, and Val86.
Protein: DP03447 (UniProt Q13177)
Region: residues 121	to 136
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The EspG-binding site on PAK2 was defined to residues 121–136, a highly conserved sequence that encodes the Iα3-helix within the kinase AID (Supplementary Fig. 8). We crystallized EspG in complex with the PAK2 Iα3-helix fragment and solved the structure to a resolution of 2.8 Å (Supplementary Table 1). EspG recognized the initial turn of the Iα3-helix whereas the remainder of the peptide adopted an extended strand conformation that lies orthogonal to the EspG six-stranded β-sheet (Fig. 3a, b).
Cross-references: PDB:3PCS
Protein: DP03447 (UniProt Q13177)
Region: residues 1	to 17
Annotation: disorder (Structural state)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
The N terminus of inactive dimeric Pak2 was associated with the highest solvent accessibility (80.0%), followed by segments that included the activation loop (52.5%) and the glycine-rich loop (49.5%). The AID (44.7%), the dimerization domain (34.4%), and the magnesium positioning loop (27.6%) were associated with slightly less solvent accessibility.
In addition, caspase cleavage and autophosphorylation dramatically and specifically increased deuteron incorporation into the N-terminal -5–17 fragment by about five deuterons, bringing the level of incorporation to 90% of the maximum, and indicating a region of high solvent exposure/flexibility (Table 1).
Protein: DP03447 (UniProt Q13177)
Region: residues 1	to 76
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy-based hydrogen-deuterium exchange evidence used in manual assertion
Supporting statements:
The regions that lack amide H/D exchange information are depicted in gray (Fig. 4b).
Protein: DP03447 (UniProt Q13177)
Region: residues 144	to 227
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy-based hydrogen-deuterium exchange evidence used in manual assertion
Supporting statements:
The regions that lack amide H/D exchange information are depicted in gray (Fig. 4b).
Protein: DP03447 (UniProt Q13177)
Region: residues 78	to 147
Annotation: disorder (Structural state)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
The N terminus of inactive dimeric Pak2 was associated with the highest solvent accessibility (80.0%), followed by segments that included the activation loop (52.5%) and the glycine-rich loop (49.5%). The AID (44.7%), the dimerization domain (34.4%), and the magnesium positioning loop (27.6%) were associated with slightly less solvent accessibility.
The AID regions corresponds to the 78-147 region and the dimerization domain to the 79-86 region.
 The AID switch domain (83–132) and the N-terminal (1–17) and the C-terminal J-helix (501–514) of autoinhibited Pak2 show that AID occupation of the active site does not prevent ligand binding to the nucleotide pocket located deep in the active-site cleft. This reflects a significant level of conformational flexibility of the AID segment occupying the active-site cleft.
Protein: DP03447 (UniProt Q13177)
Region: residues 390	to 403
Annotation: disorder (Structural state)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
The N terminus of inactive dimeric Pak2 was associated with the highest solvent accessibility (80.0%), followed by segments that included the activation loop (52.5%) and the glycine-rich loop (49.5%). The AID (44.7%), the dimerization domain (34.4%), and the magnesium positioning loop (27.6%) were associated with slightly less solvent accessibility.
The activation loop in the active site cleft is a highly solvent-accessible and flexible region (Fig. 4) and is disordered in the x-ray crystal structure of inactive Pak1 (1F3M.PDB).
The authors refer to the 390-403 region that comprises the activation loop (391-406).
Protein: DP03447 (UniProt Q13177)
Region: residues 210	to 215
Annotation: limited proteolysis display site (Disorder function)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
Inactive Pak2 was a single band of 58 kDa. Caspase cleavage of Pak2 was complete and produced two fragments, p27 and p34. Autophosphorylation of cleaved Pak2 was optimal at 7.6 mol/mol.
Caspase cleavage at Asp-212 is associated with increased amide H/D exchange in the active site (glycine-rich loop, C helix, and activation loop), the AID, and the N terminus. The increased amide H/D exchange appears to be the result of breaking two covalent bonds, Asp-212 and Ser-213, in the trans-dimerized conformation.
Protein: DP03447 (UniProt Q13177)
Region: residues 139	to 143
Annotation: phosphorylation display site (Disorder function)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
Perturbation of the AID switch by caspase cleavage could disrupt the autoinhibition and lead to autophosphorylation of Thr-402 in the activation loop and Ser-141 downstream of the AID switch.
Protein: DP03447 (UniProt Q13177)
Region: residues 399	to 403
Annotation: phosphorylation display site (Disorder function)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
Perturbation of the AID switch by caspase cleavage could disrupt the autoinhibition and lead to autophosphorylation of Thr-402 in the activation loop and Ser-141 downstream of the AID switch.
Protein: DP03448 (UniProt P56524)
Region: residues 130	to 153
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The asymmetric unit contains four copies of HDAC4, each of which folds into a single α-helix from residues 62–129, whereas residues 130–153 are disordered (Fig. 1).
Because the X-shaped diffusive streaks have a cross-angle similar to that of the four-helix bundle, one possibility is that the disordered region between residues 130 and 153 are trapped in the crystal lattice approximately along the same direction of the ordered region (residues 62 to 129) but are rotationally disordered.
Cross-references: PDB:2H8N
PDB:2O94
Protein: DP03448 (UniProt P56524)
Region: residues 729	to 760
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In addition, it was observed that amino acids 729 to 760 were not visible in the electron density maps for any of the three molecules in the asymmetric unit and were omitted
from the model because of disorder.
Cross-references: PDB:4CBT
Protein: DP03449 (UniProt P10902)
Region: residues 44	to 56
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
 The final electron density is continuous from Asn2 to Pro533, except for three protein segments (residues 44–56, 104–141 and 411–413) which lack well-defined density and were not included in the model. These three segments are located on the protein surface: the disorder of residues 44–56 is probably related to the absence of bound FAD in the crystalline enzyme (see below); residues 104–141 form part of a region known to
be highly susceptible to proteolysis [21]; and residues 411–413 belong to the linker connecting the FAD-binding domain to the helical domain (Figures 3 and 4a).
Residues 43–57, 103–142 and 410–414 are linked by thin lines, because they are at the border of the disordered polypeptide segments not included in the final model
In the apoenzyme structure, residues 44–56 are disordered
and could not be located in the electron-density map
(Figures 4a and 5).
 Various refinement protocols, including unrestrained REFMAC/ARP refinement, were tried in order to localise the regions 44–56 and 104–141. However, these residues could not be located in the density, thus suggesting that they are disordered. 
Cross-references: PDB:1CHU