LiteFold/DisProt huggingface dataset:
Protein: DP03236 (UniProt Q9UDY8)
Region: residues 466	to 481
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
While the ligand and the surrounding parts of the protein are well defined by electron density, other parts of the structure, mainly distal loops in the Ig3 domain and loops in the proximity of the active site, were disordered.
PDB:6H4A and PDB:6F7I corresponds to the crystal structures of human MALT1(329-728) in complex with MLT-748 and with MLT-747, respectively.
Cross-references: PDB:6H4A
PDB:6F7I
Protein: DP03237 (UniProt Q9BZE9)
Region: residues 498	to 553
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 313–316, 468–470 and 498–553 for ASPL-C and residues 1–20, 428–432 and 462–472 for p97-ND1 were disordered and therefore not visible in the electron density.
Cross-references: PDB:5IFS
Protein: DP03238 (UniProt P55072)
Region: residues 1	to 20
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 313–316, 468–470 and 498–553 for ASPL-C and residues 1–20, 428–432 and 462–472 for p97-ND1 were disordered and therefore not visible in the electron density.
Cross-references: PDB:5IFS
Protein: DP03238 (UniProt P55072)
Region: residues 462	to 472
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 313–316, 468–470 and 498–553 for ASPL-C and residues 1–20, 428–432 and 462–472 for p97-ND1 were disordered and therefore not visible in the electron density.
Cross-references: PDB:5IFS
Protein: DP03238 (UniProt P55072)
Region: residues 776	to 806
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Unlike others in the NSF/Cdc48/Pex AAA+ ATPase family, members of the VCP/Cdc48 subgroup contain a unique CTE that provides the binding interface for a subset of VCP cofactors (Hänzelmann and Schindelin, 2017) but has been found disordered and missing in most resolved structures (X. Zhang et al., 2000; DeLaBarre and Brunger, 2003; Davies et al., 2008; Banerjee et al., 2016; Hänzelmann and Schindelin, 2016).
This region lacks electron density in the PDB structure, indicating it is disordered.
Cross-references: EMDB:22675
PDB:7K56
Protein: DP03238 (UniProt P55072)
Region: residues 776	to 806
Annotation: flexible C-terminal tail (Disorder function)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Unlike others in the NSF/Cdc48/Pex AAA+ ATPase family, members of the VCP/Cdc48 subgroup contain a unique CTE that provides the binding interface for a subset of VCP cofactors (Hänzelmann and Schindelin, 2017) but has been found disordered and missing in most resolved structures (X. Zhang et al., 2000; DeLaBarre and Brunger, 2003; Davies et al., 2008; Banerjee et al., 2016; Hänzelmann and Schindelin, 2016).
This region lacks electron density in the PDB structure, indicating it is disordered.
(C) The domain organization and key structural elements of VCP. Each VCP monomer comprises a regulatory N-terminal domain (NTD, residues 1-187), two AAA+ ATPase domains (D1: residues 209–462 and D2: residues 481–762) and a C-terminal extension (CTE, residues 763–806).
Cross-references: EMDB:22675
PDB:7K56
Protein: DP03238 (UniProt P55072)
Region: residues 586	to 598
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 586–598 in D2 were disordered.
Residues 1–21 and 586–598 were removed from the model due to weak electron densities (Figures S3A and S3B).
This region lacks electron density in the PDB structure, indicating it is disordered.
Cross-references: EMDB:22675
PDB:7K56
Protein: DP03238 (UniProt P55072)
Region: residues 1	to 21
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 1–21 and 586–598 were removed from the model due to weak electron densities (Figures S3A and S3B).
This region lacks electron density in the PDB structure, indicating it is disordered.
Cross-references: EMDB:22675
PDB:7K56
Protein: DP03238 (UniProt P55072)
Region: residues 1	to 21
Annotation: flexible N-terminal tail (Disorder function)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 1–21 and 586–598 were removed from the model due to weak electron densities (Figures S3A and S3B).
This region lacks electron density in the PDB structure, indicating it is disordered.
Cross-references: EMDB:22675
PDB:7K56
Protein: DP03238 (UniProt P55072)
Region: residues 794	to 806
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Titration of 15N-UBXD1-PUB with the p97-C10 and p97-C13 peptide showed large (>0.2 ppm) chemical shift perturbations (CSPs) of resonances assigned to amide groups residing in the region between the second and fourth α-helix (Figure 3 and Figure S1). The interacting residues V175, A179, K180, Y181, L182, I185, L187, E191, K193, Y194, K198, L199, Q200, N201, V203, E206, R207, N209, A230, F239, E258, and L261 are mapped onto the PUB structure in Figure 3.
Protein: DP03238 (UniProt P55072)
Region: residues 797	to 806
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
In our hands, isothermal titration calorimetry (ITC) experiments showed that the peptide comprising the last 10 residues of p97 (p97–C10) interacts with UBXD1-PUB with a 1:1 stoichiometry (n = 1.1 ± 0.2) and a KD of 15 ± 5 µM, ΔH = -3255 ± 483 cal/mol, and ΔS = 10 cal/mol/K.
Protein: DP03238 (UniProt P55072)
Region: residues 802	to 806
Annotation: negative regulation of protein binding (Biological process)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
In contrast to the unmodified p97-PIM, the p97-C13 peptide carrying a phosphorylated pY805 did not show any binding in a 15N-HSQC NMR titration up to a concentration of 1.25 mM (Figure S1B), which is consistent with phosphorylation of p97-Y805 also completely abolishing binding of the PNGase and HOIP PUB domains [25,34].
Protein: DP03239 (UniProt P52874)
Region: residues 332	to 348
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
"Gray lines, framed by slanted lines, indicated sections of ceClp1 that are not included in  the crystal structure."
Cross-references: PDB:4OI2
PDB:4OHW
PDB:4OHX
PDB:4OHY
PDB:4OI0
PDB:4OI1
Protein: DP03240 (UniProt P0A8Q6)
Region: residues 1	to 20
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-terminal 20 residues of ClpS are not visible in the crystal structures; the removal of the first 17 residues produces ClpSΔN, which binds to the ClpA N-domain but no longer inhibits ClpA activity.
In the trigonal crystal, 87 out of 106 residues in ClpS can be seen in the two NCS-related heterodimers; the missing residues are from the N terminus.
The N-terminal residues from 21 to 26 extend out of the top of the cone, but residues 1–20 were not all visible.
The N-terminal chain of ClpS extends along the N-domain parallel to helix H3 until the density disappears; this configuration would probably place the missing residues near the C terminus of the N-domain and away from the acidic loop connecting the two halves (Fig. 2A).
Cross-references: PDB:1MBU
PDB:1MBV
PDB:1MBX
Protein: DP03240 (UniProt P0A8Q6)
Region: residues 1	to 17
Annotation: molecular function inhibitor activity (Molecular function)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
The N-terminal 20 residues of ClpS are not visible in the crystal structures; the removal of the first 17 residues produces ClpSΔN, which binds to the ClpA N-domain but no longer inhibits ClpA activity.
When the N-terminal 17 amino acids of ClpS were removed by lysylendopeptidase C treatment, the resulting ClpSΔN could still bind to ClpA and the isolated N-domain of ClpA (Fig. 1, A and B); however, ClpSΔN was no longer able to inhibit proteolytic activity of ClpAP. Table III shows that both casein and green fluorescent protein-SsrA degradation were unaffected by ClpSΔN.
Protein: DP03240 (UniProt P0A8Q6)
Region: residues 1	to 22
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The structure of the complex crystallized in tetragonal space group was solved by molecular replacement using the refined model of the orthorhombic space group. Although this structure could be refined at 2.3 Å resolution to a crystallographic R-factor of 25.2 (Rfree = 29.4%), several residues were not visible, namely the N-terminal residues of ClpS (1–22) and three residues in the N-domain of ClpA (73–75).
Cross-references: PDB:1MG9
Protein: DP03240 (UniProt P0A8Q6)
Region: residues 1	to 20
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the final structure, five residues of ClpS (16–20) and three residues in ClpA161 (73–75) were replaced with Ala because they showed only main chain density. The final structure consists of 146 of the 161 residues from ClpA161, 91 of 106 residues from ClpS and 49 ordered solvent molecules.
The N-terminal region of ClpS is poorly defined; the first 15 residues are not visible in the electron density maps, and the next 13 residues (16–28), although present, form an extended coiled protein chain.
Cross-references: PDB:1LZW
Protein: DP03241 (UniProt P0ABH9)
Region: residues 143	to 167
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
There are several disordered regions in the ClpA structure; all of them are loops connecting secondary structure elements or between domains (Fig. 1b).
The electron density for the 25 residues connecting the N-domain and D1 was not visible, but we were able to identify the cognate N-domain based on three criteria: the distance between the C-terminal residues of the N-domains and the first determined residue of D1, the surface area buried by each N-domain-D1D2 contact, and the location of contact interface.
Cross-references: PDB:1KSF
Protein: DP03241 (UniProt P0ABH9)
Region: residues 611	to 623
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
There are several disordered regions in the ClpA structure; all of them are loops connecting secondary structure elements or between domains (Fig. 1b).
Other regions for which density was not well defined included residues 252–255, residues 295–300, and notably residues 611–625 (Fig. 1b).
The “ClpP loop,” containing the sequence IGL, which has been implicated in activation of ClpP activity by ClpA (25, 26), was not visible in the crystal. However, residues 611 and 624, which flank the loop, are located on the distal surface of D2 at about 30–35 Å from the center (Fig. 5, b and d).
Residues 611-623 are not visible in the electron density map.
Cross-references: PDB:1KSF
Protein: DP03241 (UniProt P0ABH9)
Region: residues 142	to 168
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
ClpA consists of three functional domains: an N-terminal domain and two ATPase domains, D1 and D2. The N-domain is attached to D1 by a mobile linker and is made up of two tightly bound, identically folded a-helical bundles related by a pseudo 2-fold symmetry.
Residues 142-168 are not visible in the electron density map.
Cross-references: PDB:1R6B
Protein: DP03241 (UniProt P0ABH9)
Region: residues 143	to 167
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
There are several disordered regions in the ClpA structure; all of them are loops connecting secondary structure elements or between domains (Fig. 1b).
The full length ClpA subunit consists of five tandemly linked structural domains (Fig. 1a) corresponding to three functional groups: an N-domain and two AAA ATPase modules. The N-domain has 142 residues; the first AAA ATPase module (D1) has 270 residues and the second ATPase module (D2) contains 319 residues, each consisting of a large and a small sub-domain (Fig. 1b).
The electron density for the 25 residues connecting the N-domain and D1 was not visible, but we were able to identify the cognate N-domain based on three criteria: the distance between the C-terminal residues of the N-domains and the first determined residue of D1, the surface area buried by each N-domain-D1D2 contact, and the location of contact interface.
Protein: DP03242 (UniProt P23588)
Region: residues 1	to 96
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the structure, no additional unfilled density is observed next to eS28 and eIF3d (Supplementary Figure S7B), indicating that the eIF4B BD is rather flexible.
Cross-references: PDB:6FEC
Protein: DP03242 (UniProt P23588)
Region: residues 172	to 611
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
 "In the structure, no additional unfilled density is observed next to eS28 and eIF3d (Supplementary Figure S7B), indicating that the eIF4B BD is rather flexible." 
Cross-references: PDB:6FEC
Protein: DP03242 (UniProt P23588)
Region: residues 333	to 611
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Based on an initial 1H,15N-HSQC spectrum acquired for the complete C-terminal region of human eIF4B (eIF4B-CTR, residues 333–611), it was evident that the backbone amide 1HN chemical shift values were restricted to 8.0-8.5 ppm (Fig. 1A), and thus the construct was predominantly disordered.
Cross-references: BMRB:51957
BMRB:51952
BMRB:51953
Protein: DP03243 (UniProt Q68D10)
Region: residues 571	to 604
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows this region lacks electron density, indicating it is disordered.
Cross-references: PDB:5BS7
Protein: DP03245 (UniProt Q9UQ35)
Region: residues 31	to 2752
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The authors do not specify in the paper that the 31 - 2752 region is disordered, but the specified residues are missing in the PDB.
The SRM300 protein is part of human spliceosomal C complex, composed of 34 other macromolecules.
Cross-references: PDB:5MQF
Protein: DP03245 (UniProt Q9UQ35)
Region: residues 27	to 2752
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
PDB - unmodeled residue 27-2752
Cross-references: PDB:5XJC
Protein: DP03245 (UniProt Q9UQ35)
Region: residues 27	to 2752
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
PDB - Unmodeled residue 27-2752
Cross-references: PDB:5YZG
Protein: DP03245 (UniProt Q9UQ35)
Region: residues 27	to 2752
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
PDB - unmodeled residues 27 - 2752
Cross-references: PDB:5Z56
Protein: DP03245 (UniProt Q9UQ35)
Region: residues 35	to 2752
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
PDB - unmodeled residues 35 - 2752
Cross-references: PDB:6FF4
Protein: DP03245 (UniProt Q9UQ35)
Region: residues 27	to 2752
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
PDB - unmodeled residues 27- 2752
Cross-references: PDB:6ICZ
Protein: DP03246 (UniProt O75475)
Region: residues 430	to 471
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy-based hydrogen-deuterium exchange evidence used in manual assertion
Supporting statements:
Scarcity of NOEs observed for residues C-terminal to Gly430, poor chemical shift dispersion on the 2D 1H-15N HSQC spectrum, and fast hydrogen-deuterium exchange of the main chain amide protons collectively suggested that residues 430–471 were not involved in a stable fold
Cross-references: PDB:1Z9E
Protein: DP03246 (UniProt O75475)
Region: residues 92	to 135
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB structure shows this region lacks electron density, indicating it is disordered.
Cross-references: PDB:4FU6
Protein: DP03248 (UniProt Q9NYV4)
Region: residues 1023	to 1063
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows this region lacks electron density, indicating it is disordered.
Cross-references: PDB:6CKX
Protein: DP03249 (UniProt Q96RJ3)
Region: residues 1	to 19
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Nineteen residues, including Cys19 through Leu37, define the structured core of the BR3 ECD, while the rest of the N- and C-terminal residues are highly flexible (Figure 1)
Cross-references: PDB:1OSX
Protein: DP03249 (UniProt Q96RJ3)
Region: residues 37	to 184
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Nineteen residues, including Cys19 through Leu37, define the structured core of the BR3 ECD, while the rest of the N- and C-terminal residues are highly flexible (Figure 1)
Cross-references: PDB:1OSX
Protein: DP03250 (UniProt Q9UBW5)
Region: residues 1	to 37
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model included residues 37 to 238, that is, the N-terminal amphipathic helix was disordered in both subunits
Cross-references: PDB:4I1Q
Protein: DP03251 (UniProt Q8N300)
Region: residues 1	to 23
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
 Superimposition of the structures of V2c–SVBP (colored as in Fig. 1a) and V2–SVBP (colored in wheat) in cartoon representation. The rmsd of the two superimposed structures is 0.29 Å. The comparison reveals that the structures of V2c and full-length V2 are almost the same, and that the N- and C-terminal flanking regions of V2 are disordered. 
Cross-references: PDB:6J4S
PDB:6QBY
PDB:6J4O
PDB:6J4P
PDB:6J4U
Protein: DP03253 (UniProt P08799)
Region: residues 703	to 735
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
PDB - unmodeled residue 703 -735
Cross-references: PDB:1YV3
Protein: DP03253 (UniProt P08799)
Region: residues 748	to 762
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
PDB - unmodeled residue 748 -762
Cross-references: PDB:1YV3
Protein: DP03253 (UniProt P08799)
Region: residues 701	to 732
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
PDB - unmodeled residue 701-732
S236A mutant
Cross-references: PDB:3MYH
Protein: DP03253 (UniProt P08799)
Region: residues 748	to 762
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
PDB - unmodeled residue 748-762
S236A mutant
Cross-references: PDB:3MYH
Protein: DP03253 (UniProt P08799)
Region: residues 701	to 732
Annotation: order (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
PDB - residues 701-732 ordered by crystal contact in space group P21212
S236A mutant
Cross-references: PDB:3MYL
Protein: DP03253 (UniProt P08799)
Region: residues 748	to 759
Annotation: order (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
PDB - residues 748-759 ordered by crystal contact in space group P21212
S236A mutant
Cross-references: PDB:3MYL
Protein: DP03253 (UniProt P08799)
Region: residues 698	to 735
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
PDB - unmodeled residues 698-735 
S236A mutant
Cross-references: PDB:3MYK
Protein: DP03253 (UniProt P08799)
Region: residues 750	to 762
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
PDB - unmodeled residues 750-762
S236A mutant
Cross-references: PDB:3MYK
Protein: DP03253 (UniProt P08799)
Region: residues 702	to 721
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
PDB - unmodeled residues 702-721
R238E.E459R mutant
Cross-references: PDB:4PJK
Protein: DP03253 (UniProt P08799)
Region: residues 748	to 761
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
PDB - unmodeled residues 748-761
R238E.E459R mutant
Cross-references: PDB:4PJK