LiteFold/DisProt huggingface dataset:
Protein: DP03449 (UniProt P10902)
Region: residues 104	to 141
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
Protein: DP03450 (UniProt P0DTC4)
Region: residues 61	to 75
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 1H/15N heteronuclear NOE data also shows that residues 2–7, before the start of the N-terminal helix, and residues 61–75 following the end of the C-terminal helix exhibit gradients of increasing motion towards the termini, although even the terminal residues do not appear to be highly mobile and unstructured, as is sometimes the case in this class of proteins [32,50].
Protein: DP03451 (UniProt P21675-1)
Region: residues 1626	to 1638
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues COOH-terminal to the bromodomain motifs (residues 1625 to 1638) were not visible in the experimental map and presumably are disordered. 
Cross-references: PDB:1EQF
Protein: DP03451 (UniProt P21675-1)
Region: residues 972	to 1053
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
There is a small protein density contacting the minor groove of the Inr (Fig. 2a, d). We propose that it corresponds to the portion of TAF1 between residues 993–1075, which is disordered in the crystal structure but is well conserved among metazoans and is predicted to be ~50% α-helical (Extended Data Fig. 4c–e).
The IDR chracterized in the publication and spanning residues 993-1075 of the isoform 2 corresponds to region 972-1053 of the canonical sequence, since the isoform 2 differs from the canonical sequence as follows 177-177: G → GVSENGEGIILPSIIAPSSLAS
Cross-references: PDB:5FUR
Protein: DP03452 (UniProt Q6P1X5)
Region: residues 977	to 1199
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
b, Domain arrangement of TAF2, including the four subdomains of the APD (D1-4), and the C-terminal intrinsically-disordered region (IDR).
Cross-references: PDB:5FUR
Protein: DP03453 (UniProt P51513)
Region: residues 125	to 143
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In Nova KH1-KH2, the interdomain linker is considerably longer (26-aa)  and  partially  disordered  in  the  crystal,  compared  to  a  10-aa  linker  in  IMP1 KH3/4, and a 14-aa linker in PCBP2 KH1/2.
Cross-references: PDB:2ANN
PDB:2ANR
Protein: DP03454 (UniProt Q9UBP0)
Region: residues 228	to 323
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-terminal 96 residues of the construct used to obtain the crystals in this study were not visible in the final structure. As this region of the protein is predicted to have very little secondary structure (Kabsch, 1983), it was unclear whether the entire construct had been crystallized and simply contained a disordered N-terminus, or the N- terminal amino acids were actually absent.
Additionally, in a sample of purified spastin protein, several low molecular weight bands were detected, indicating that the N-terminus of this construct is degraded or cleaved.
Cross-references: PDB:3VFD
Protein: DP03454 (UniProt Q9UBP0)
Region: residues 270	to 328
Annotation: protein binding (Molecular function)
Evidence: cross-linking evidence used in manual assertion
Supporting statements:
The N-terminal region consists of four subdomains (see Fig. 1 A for schematic): the Atlastin binding domain (Evans et al., 2006), the MIT domain, alternatively spliced exon 4 (Charvin et al., 2003), and as we show in Fig. 2, an MTBD that is both necessary for MT severing and sufficient for MT association.
In contrast, ΔMTBD Spastin neither bound nor severed MTs, demonstrating that aa 270–328 are necessary for MT severing in vitro. 
In contrast, deletion of the first 328 amino acids did abolish severing activity,  as  the  transfected  cell  still  has  an  MT  array.  This  suggested  that  the approximate boundaries for a MTBD are between aa 280 and 328. 
We next examined whether the MTBD was sufficient to confer MT association both in cells and in vitro. In transfection experiments, 1–328 stop Spastin but not 1–279 stop Spastin 
decorated  MTs,  suggesting  that  amino  acids  280–328  are  important for MT binding (Fig. 2 C).
Protein: DP03454 (UniProt Q9UBP0)
Region: residues 270	to 328
Annotation: protein binding (Molecular function)
Evidence: bait-prey hybrid interaction evidence used in manual assertion
Supporting statements:
In addition to the pore interaction with tubulin, we defi ne an N-terminal MT binding domain (MTBD) in  Spastin  that  mediates  the  attachment  of  Spastin  to  the  MT.  
This interaction is also required for severing.
In contrast, ∆MTBD Spastin neither bound nor severed MTs, demonstrating that aa 270–328 are necessary for MT severing in vitro
In contrast, deletion of the first 328 amino acids did abolish severing activity,  as  the  transfected  cell  still  has  an  MT  array.
Our  deletion  analysis  revealed  the  existence  of  an  N-terminal MTBD in Spastin (aa 270–328) that is required for MT-severing activity in vivo and in vitro.
Protein: DP03454 (UniProt Q9UBP0)
Region: residues 229	to 322
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Similar to the result of a previous structural study of human spastin [30], only the AAA domain was visible in the electron density, while the MTBD region was not visible. 
Cross-references: PDB:5Z6Q
Protein: DP03455 (UniProt O00189)
Region: residues 160	to 184
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
A close inspection to the crystal structure of either wild-type μ4 (pdb entry 3l81; [18]) or μ4-D190A revealed that the SDQSQKNEVF sequence is at the end of the disordered N-terminal region, in which only the NEVF portion is visible in the crystal structure (Figure 6E)
Cross-references: PDB:4MDR
Protein: DP03455 (UniProt O00189)
Region: residues 384	to 399
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
(B) Sequence alignment of the C-terminal domain of the μ subunits of known crystal structure depicting critical residues at the corresponding μ2- and μ4-binding sites. Disordered loops are in yellow letters, and arrows and cylinders represent β-strands and α-helices, respectively. M.m., Mus musculus; R.n., Rattus norvegicus; H.s., Homo sapiens.
Likewise, the SASPLGLGPA sequence is part of a disordered loop followed by a well-structured region, with the LGLGPA portion visible in the crystal structure (Figure 6E). 
Cross-references: PDB:4MDR
Protein: DP03455 (UniProt O00189)
Region: residues 384	to 399
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Disordered loops are in green (P388-P399) and red (P430-N 435) letters in µ4 and
in green (V221-G237) and blue (K256-S259) letters in µ2, and are represented in the respective colors as dashed lines in (A).
Cross-references: PDB:3L81
Protein: DP03456 (UniProt P27635)
Region: residues 95	to 123
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The internal missing part, His95– Gln123, corresponds to the internal loop of the TthL16 NMR structure. 
The invisible electron density of His95–Gln123 implies that the internal loop of eukaryotic L10 is also flexible in the free state and assumes a structure by binding on the ribosome.
The internal disordered region (residues His95–Gln123) is indicated by arrows.
The internal loop of L10CD, Arg98–Gln123, was removed from the search model in advance because the loop was expected to be unstructured considering the NMR analysis of bacterial L16.
Cross-references: PDB:2PA2
Protein: DP03457 (UniProt Q29502)
Region: residues 125	to 238
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
The entire mass spectrum of pepsin-digested Pak2 is shown in Fig. 3a. 30 of 42 identified peptides had m/z ratios that were sufficiently different from one another and of sufficient magnitude to use in the amide H/D exchange experiments discussed below. These peptides covered 50% of the primary sequence of Pak2, including all or part of the following regions: the N-terminal region, dimerization domain, AID, glycine-rich loop, C helix, catalytic loop, magnesium-positioning loop, activation loop, and regions without an identified function.
FIGURE 4. Solvent accessibility of inactive Pak2. a, the Pak2 sequence and the peptic peptides identified after 10 min of H/D exchange of Pak2 are color coded according to level of deuterium incorporation into exchangeable amides.
Figure 4 shows that the region ranging 125-238 is completely digested by pepsin.
Protein: DP03457 (UniProt Q29502)
Region: residues 18	to 57
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
FIGURE 4. Solvent accessibility of inactive Pak2. a, the Pak2 sequence and the peptic peptides identified after 10 min of H/D exchange of Pak2 are color coded according to level of deuterium incorporation into exchangeable amides.
The entire mass spectrum of pepsin-digested Pak2 is shown in Fig. 3a. 30 of 42 identified peptides had m/z ratios that were sufficiently different from one another and of sufficient magnitude to use in the amide H/D exchange experiments discussed below. These peptides covered 50% of the primary sequence of Pak2, including all or part of the following regions: the N-terminal region, dimerization domain, AID, glycine-rich loop, C helix, catalytic loop, magnesium-positioning loop, activation loop, and regions without an identified function.
Figure 4 shows that the region ranging 18-57 is completely digested by pepsin.
Protein: DP03457 (UniProt Q29502)
Region: residues 253	to 281
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
FIGURE 4. Solvent accessibility of inactive Pak2. a, the Pak2 sequence and the peptic peptides identified after 10 min of H/D exchange of Pak2 are color coded according to level of deuterium incorporation into exchangeable amides.
The entire mass spectrum of pepsin-digested Pak2 is shown in Fig. 3a. 30 of 42 identified peptides had m/z ratios that were sufficiently different from one another and of sufficient magnitude to use in the amide H/D exchange experiments discussed below. These peptides covered 50% of the primary sequence of Pak2, including all or part of the following regions: the N-terminal region, dimerization domain, AID, glycine-rich loop, C helix, catalytic loop, magnesium-positioning loop, activation loop, and regions without an identified function.
Figure 4 shows that the region ranging 253-281 is completely digested by pepsin.
Protein: DP03457 (UniProt Q29502)
Region: residues 310	to 356
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
FIGURE 4. Solvent accessibility of inactive Pak2. a, the Pak2 sequence and the peptic peptides identified after 10 min of H/D exchange of Pak2 are color coded according to level of deuterium incorporation into exchangeable amides.
The entire mass spectrum of pepsin-digested Pak2 is shown in Fig. 3a. 30 of 42 identified peptides had m/z ratios that were sufficiently different from one another and of sufficient magnitude to use in the amide H/D exchange experiments discussed below. These peptides covered 50% of the primary sequence of Pak2, including all or part of the following regions: the N-terminal region, dimerization domain, AID, glycine-rich loop, C helix, catalytic loop, magnesium-positioning loop, activation loop, and regions without an identified function.
Figure 4 shows that the region ranging 310-356 is completely digested by pepsin.
Protein: DP03457 (UniProt Q29502)
Region: residues 1	to 17
Annotation: order to disorder (Structural transition)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
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: DP03457 (UniProt Q29502)
Region: residues 1	to 17
Annotation: disorder (Structural state)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
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: DP03458 (UniProt P0DMC7)
Region: residues 133	to 147
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
 The first N-terminal residue and 15 C-terminal residues comprising part of the inter-domain linker were not ordered in the electron density map. 
Cross-references: PDB:5I4C
Protein: DP03459 (UniProt Q15542)
Region: residues 381	to 416
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Disordered loops are drawn as grey dashed lines.
The final model includes residues 207-800 of TAF5 (residues 194-206, 381-416 and 748-753 were not modeled due to poor definition), residues 6-92 of TAF6 and residues 5-120 of TAF9.
Cross-references: PDB:6F3T
Protein: DP03459 (UniProt Q15542)
Region: residues 194	to 206
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 residues 207-800 of TAF5 (residues 194-206, 381-416 and 748-753 were not modeled due to poor definition), residues 6-92 of TAF6 and residues 5-120 of TAF9.
Cross-references: PDB:6F3T
Protein: DP03460 (UniProt P0DTC7)
Region: residues 83	to 96
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final structure, with a visible electron density spanning residues 14–82, was refined to R factor and R-free values of 0.201 and 0.246, respectively.
Cross-references: PDB:7CI3
Protein: DP03464 (UniProt Q04195)
Region: residues 445	to 465
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Amino acids 112–158, 348–352, and 445–465 were present in the crystal and presumed disordered.
Cross-references: PDB:3I2D
Protein: DP03465 (UniProt Q9T0N8)
Region: residues 19	to 32
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The region following the signal peptide (1-18) is missing in the coordinates of the 4 structures (see cross references).
Cross-references: PDB:3S1C
PDB:3S1D
PDB:3S1F
PDB:3S1E
Protein: DP03465 (UniProt Q9T0N8)
Region: residues 19	to 32
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The region following the signal peptide (1-18) is missing in the coordinates of the 3 structures (see cross references).
Cross-references: PDB:2QPM
PDB:2QKN
PDB:3KJM
Protein: DP03465 (UniProt Q9T0N8)
Region: residues 19	to 39
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-terminal 40 amino acid residues are not visible in the electron density map, in agreement with the observation that CKX is produced as a precursor protein undergoing an N-terminal cleavage upon processing.
The protein has an 18-residue signal peptide, which is not present in the structure of the mature form. The remaining residues (19-39) are disordered and were not modeled.
Cross-references: PDB:1W1R
PDB:1W1S
PDB:1W1Q
PDB:1W1O
Protein: DP03465 (UniProt Q9T0N8)
Region: residues 19	to 31
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
It was possible to fit to electron density an additional part, GRPWPASLA, at the N-terminus, leaving only 12 amino acids disordered. In addition, the sequence segments DNATAAA (amino acids 337–343) and VAP (amino acids 462–464), all missing in the 1W1O Protein Data Bank (PDB) file, could be constructed.
Since the protein has an 18-residue signal peptide, there are 13 disordered residues for structure 3BW7 and 14 for 3C0P.
Cross-references: PDB:3BW7
Protein: DP03465 (UniProt Q9T0N8)
Region: residues 19	to 32
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
It was possible to fit to electron density an additional part, GRPWPASLA, at the N-terminus, leaving only 12 amino acids disordered. In addition, the sequence segments DNATAAA (amino acids 337–343) and VAP (amino acids 462–464), all missing in the 1W1O Protein Data Bank (PDB) file, could be constructed.
Since the protein has an 18-residue signal peptide, there are 13 disordered residues for structure 3BW7 and 14 for 3C0P.
Cross-references: PDB:3C0P
Protein: DP03466 (UniProt E3T1W8)
Region: residues 292	to 319
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The helix-loop-helix region from residues 294-325 in ZmCKO1 (shown with red arrows) adopts a different conformation in ZmCKO2 (PDB ID: 4ML8, this work) and is disordered in ZmCKO4a (PDB ID 4OAL, this work).
Cross-references: PDB:4OAL
Protein: DP03466 (UniProt E3T1W8)
Region: residues 292	to 319
Annotation: molecular function regulator (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The helix-loop-helix region from residues 294-325 in ZmCKO1 (shown with red arrows) adopts a different conformation in ZmCKO2 (PDB ID: 4ML8, this work) and is disordered in ZmCKO4a (PDB ID 4OAL, this work).
This region, which is well deﬁned in the ZmCKO1 structure, is disordered in the high resolution structures of ZmCKO4a and ZmCKO2
and adopts a different conformation in the low resolution structure of ZmCKO2 (Fig. 4A). The region delineating the substrate entrance comprises residues surrounding the ribose moiety of cytokinin substrate (N303 and T304 in ZmCKO1) and is most likely responsible for the kinetic differences between the E381 variants and the ZmCKO isoforms.
Cross-references: PDB:4OAL
Protein: DP03466 (UniProt E3T1W8)
Region: residues 292	to 318
Annotation: molecular function regulator (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The helix-loop-helix region from residues 294-325 in ZmCKO1 (shown with red arrows) adopts a different conformation in ZmCKO2 (PDB ID: 4ML8, this work) and is disordered in ZmCKO4a (PDB ID 4OAL, this work).
This region, which is well deﬁned in the ZmCKO1 structure, is disordered in the high resolution structures of ZmCKO4a and ZmCKO2
and adopts a different conformation in the low resolution structure of ZmCKO2 (Fig. 4A). The region delineating the substrate entrance comprises residues surrounding the ribose moiety of cytokinin substrate (N303 and T304 in ZmCKO1) and is most likely responsible for the kinetic differences between the E381 variants and the ZmCKO isoforms.
Cross-references: PDB:4O95
Protein: DP03466 (UniProt E3T1W8)
Region: residues 292	to 318
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The helix-loop-helix region from residues 294-325 in ZmCKO1 (shown with red arrows) adopts a different conformation in ZmCKO2 (PDB ID: 4ML8, this work) and is disordered in ZmCKO4a (PDB ID 4OAL, this work).
Cross-references: PDB:4O95
Protein: DP03466 (UniProt E3T1W8)
Region: residues 532	to 541
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The C-terminal decapeptide is unmodelled in both structures (see cross references) of this enzyme.
Cross-references: PDB:4O95
PDB:4OAL
Protein: DP03466 (UniProt E3T1W8)
Region: residues 22	to 38
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-terminal segment, following the signal peptide (1-21), is unmodelled in both structures (see cross references) of this enzyme.
Cross-references: PDB:4O95
PDB:4OAL
Protein: DP03466 (UniProt E3T1W8)
Region: residues 22	to 39
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-terminal segment, following the signal peptide (1-21), is unmodelled in the structure (see cross reference) of this enzyme.
Cross-references: PDB:5HHZ