LiteFold/DisProt huggingface dataset:
Protein: DP03797 (UniProt Q4QDS0)
Region: residues 288	to 328
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, indicanting it is disordered.
Cross-references: PDB:5XIL
Protein: DP03797 (UniProt Q4QDS0)
Region: residues 676	to 687
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, indicanting it is disordered.
Cross-references: PDB:5XIL
Protein: DP03798 (UniProt Q711P7)
Region: residues 252	to 262
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Molecule A has three disordered, presumably flexible loops, comprising residues 251-263, 551-579, 614-625. Molecule B has five loops missing, between 227 and 234, 250 and 263, 551 and 578, 617 and 625, and 632 and 637.
Cross-references: PDB:2VOB
Protein: DP03798 (UniProt Q711P7)
Region: residues 552	to 577
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Molecule A has three disordered, presumably flexible loops, comprising residues 251-263, 551-579, 614-625. Molecule B has five loops missing, between 227 and 234, 250 and 263, 551 and 578, 617 and 625, and 632 and 637.
Cross-references: PDB:2VOB
Protein: DP03799 (UniProt Q9U5N6)
Region: residues 358	to 370
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In both the T. brucei and L. mexicana aldolases, the 11 Cterminal residues were not visible in the density of any subunit.
Cross-references: PDB:1EPX
Protein: DP03800 (UniProt P42861)
Region: residues 1	to 48
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
For the first 44 and the last residue – Leu605 – of PGI-Lm (Fig. 2), no electron density was distinguishable in the 2σA|Fo|-D|Fc| map of both chains of the homodimer. The absence of continuous electron density for residues 1–44 indicates that the N-terminal sequence is not ordered. Based on the electron density map and sequence alignment, four additional residues (Val45 to Ser48) could be added to that region of PGI-Lm (Fig. 2).
Cross-references: PDB:1T10
Protein: DP03801 (UniProt O97193)
Region: residues 340	to 351
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The terminal residues 1–7 and 336–350 as well as the C-terminal His-tag were not built into the structure models due to the lack of interpretable electron density
The PDB shows this region constitutes the IDR conserved by all chains obtained.
Cross-references: PDB:5OEZ
PDB:5OFU
PDB:5OEY
Protein: DP03801 (UniProt O97193)
Region: residues 52	to 70
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The dynamic loop (residues 52–71) was found to adopt an engaged conformation (Fig. 4b), in contrast to the apoenzyme structure where the dynamic loop was found to be disordered in two of the chains.
Cross-references: PDB:5OEZ
Protein: DP03801 (UniProt O97193)
Region: residues 52	to 61
Annotation: disorder to order (Structural transition)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
As a result of this rotation, the dynamic loop (residues 52–71) is pulled out from the active site in a canonical “disengaged conformation” [33], which is stabilized by the diagonal subunit.
Cross-references: PDB:5OFU
Protein: DP03801 (UniProt O97193)
Region: residues 61	to 70
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
As a result of this rotation, the dynamic loop (residues 52–71) is pulled out from the active site in a canonical “disengaged conformation” [33], which is stabilized by the diagonal subunit.
The “disengaged-conformation” (in which most of the loop is disordered in the AMP-bound structure) is prevented from adopting an active conformation by the strong hydrogen bonded network around Arg48 which hydrogen bonds to the dynamic loop (residue 52) (Fig. 5d) and pointing the remainder of the loop out into solvent.
Cross-references: PDB:5OFU
Protein: DP03802 (UniProt A0A1L8HGL2)
Region: residues 738	to 1171
Annotation: disorder (Structural state)
Evidence: electron microscopy evidence used in manual assertion
Supporting statements:
(B) Cryo-EM structure of Nup358-NTD2 at 3.0-Å resolution. Left: Resolution map of Nup358-NTD2. The local resolutions might be slightly inflated due to a variety of factors. Please refer to fig. S7C for representative densities. Right: Domain structure of Nup358. UR, unstructured region; FR, functional region. The terminal residues are labeled. Four surface motifs of Nup358-NTD2 (N-hook, loop-1, clip helices, loop-2), which mediate the cross-talk between Nup358-NTD2 and ACE1 proteins within the CR, are color coded.
Cross-references: PDB:7FIL
EMDB:31602
Protein: DP03803 (UniProt Q24459)
Region: residues 339	to 354
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
C: {1H-}-15N heteronuclear NOE indicates flexible N- and C-termini of Pcl-Tudor. 
Cross-references: PDB:2XK0
BMRB:17050
Protein: DP03804 (UniProt Q9VVI2)
Region: residues 71	to 101
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
The remaining C-terminal extension (30 residues) is unstructured.
Cross-references: PDB:2RM4
BMRB:11009
Protein: DP03804 (UniProt Q9VVI2)
Region: residues 71	to 101
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
The two structures confirm and confine the EDC3 LSm domain as an independent folding unit and suggest that residues beyond HsP68 and DmA71 are part of the unstructured region of EDC3 which links the LSm domain to the predicted FDF domain.
Cross-references: BMRB:11009
PDB:2RM4
Protein: DP03804 (UniProt Q9VVI2)
Region: residues 101	to 338
Annotation: disorder (Structural state)
Evidence: author inference used in manual assertion
Supporting statements:
Members of the EDC3 protein family have a modular domain organization made up of an N-terminal LSm domain, a central FDF domain and a C-terminal YjeF-N domain (Fig.1A). The LSm and FDF domains are connected by a sequence rich in glutamine, asparagine, glycine, and arginine residues, which is likely to be unstructured (Fig.1A, linker) (1, 2).
(A) Domain architecture of EDC3. EDC3 orthologs contain three classified globular domains: an LSm domain, an FDF domain, and a YjeF-N-type Rossman fold domain. The LSm and FDF domains are connected by a low-complexity linker region. 
The two structures confirm and confine the EDC3 LSm domain as an independent folding unit and suggest that residues beyond HsP68 and DmA71 are part of the unstructured region of EDC3 which links the LSm domain to the predicted FDF domain.
Protein: DP03804 (UniProt Q9VVI2)
Region: residues 101	to 338
Annotation: flexible linker (Disorder function)
Evidence: author inference used in manual assertion
Supporting statements:
Members of the EDC3 protein family have a modular domain organization made up of an N-terminal LSm domain, a central FDF domain and a C-terminal YjeF-N domain (Fig. ​(Fig.1A).1A). The LSm and FDF domains are connected by a sequence rich in glutamine, asparagine, glycine, and arginine residues, which is likely to be unstructured (Fig. ​(Fig.1A,1A, linker) (1, 2).
(A) Domain architecture of EDC3. EDC3 orthologs contain three classified globular domains: an LSm domain, an FDF domain, and a YjeF-N-type Rossman fold domain. The LSm and FDF domains are connected by a low-complexity linker region. 
The two structures confirm and confine the EDC3 LSm domain as an independent folding unit and suggest that residues beyond HsP68 and DmA71 are part of the unstructured region of EDC3 which links the LSm domain to the predicted FDF domain.
Protein: DP03805 (UniProt Q15858)
Region: residues 417	to 725
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
For both structures, side chains could be assigned for residues 114 to 1768 except for the intracellular linkers I-II (residues 418 to 725) and II-III (residues 973 to 1174).
In total, 1140 residues for Nav 1.7, 173 residues for β1, and 120 residues for β2 were assigned with side chains, and 10 sugar moieties were built. The N-terminal 113 residues, intracellular I-II linker (residues 418-725), II-III linker (residues 973-1174), and C-terminal sequences after Glu1768 are invisible in Na v1.7.
Cross-references: PDB:6J8H
PDB:6J8I
PDB:6J8J
PDB:6J8G
Protein: DP03805 (UniProt Q15858)
Region: residues 973	to 1174
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
For both structures, side chains could be assigned for residues 114 to 1768 except for the intracellular linkers I-II (residues 418 to 725) and II-III (residues 973 to 1174).
In total, 1140 residues for Nav 1.7, 173 residues for β1, and 120 residues for β2 were assigned with side chains, and 10 sugar moieties were built. The N-terminal 113 residues, intracellular I-II linker (residues 418-725), II-III linker (residues 973-1174), and C-terminal sequences after Glu1768 are invisible in Na v1.7.
Cross-references: PDB:6J8H
PDB:6J8I
PDB:6J8J
PDB:6J8G
Protein: DP03805 (UniProt Q15858)
Region: residues 973	to 1174
Annotation: flexible linker (Disorder function)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
For both structures, side chains could be assigned for residues 114 to 1768 except for the intracellular linkers I-II (residues 418 to 725) and II-III (residues 973 to 1174).
In total, 1140 residues for Nav 1.7, 173 residues for β1, and 120 residues for β2 were assigned with side chains, and 10 sugar moieties were built. The N-terminal 113 residues, intracellular I-II linker (residues 418-725), II-III linker (residues 973-1174), and C-terminal sequences after Glu1768 are invisible in Na v1.7.
Cross-references: PDB:6J8H
PDB:6J8I
PDB:6J8J
PDB:6J8G
Protein: DP03805 (UniProt Q15858)
Region: residues 417	to 725
Annotation: flexible linker (Disorder function)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
For both structures, side chains could be assigned for residues 114 to 1768 except for the intracellular linkers I-II (residues 418 to 725) and II-III (residues 973 to 1174).
In total, 1140 residues for Nav 1.7, 173 residues for β1, and 120 residues for β2 were assigned with side chains, and 10 sugar moieties were built. The N-terminal 113 residues, intracellular I-II linker (residues 418-725), II-III linker (residues 973-1174), and C-terminal sequences after Glu1768 are invisible in Na v1.7.
Cross-references: PDB:6J8H
PDB:6J8I
PDB:6J8J
PDB:6J8G
Protein: DP03805 (UniProt Q15858)
Region: residues 1	to 113
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In total, 1140 residues for Nav 1.7, 173 residues for β1, and 120 residues for β2 were assigned with side chains, and 10 sugar moieties were built. The N-terminal 113 residues, intracellular I-II linker (residues 418-725), II-III linker (residues 973-1174), and C-terminal sequences after Glu1768 are invisible in Na v1.7.
Cross-references: PDB:6J8H
PDB:6J8I
PDB:6J8J
PDB:6J8G
Protein: DP03805 (UniProt Q15858)
Region: residues 1769	to 1988
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In total, 1140 residues for Nav 1.7, 173 residues for β1, and 120 residues for β2 were assigned with side chains, and 10 sugar moieties were built. The N-terminal 113 residues, intracellular I-II linker (residues 418-725), II-III linker (residues 973-1174), and C-terminal sequences after Glu1768 are invisible in Na v1.7.
Cross-references: PDB:6J8H
PDB:6J8I
PDB:6J8J
PDB:6J8G
Protein: DP03806 (UniProt Q3U8S1)
Region: residues 293	to 365
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
CD spectroscopy shows that CD44ct is largely disordered without apparent secondary structure features (Fig. 1D).
Protein: DP03806 (UniProt Q3U8S1)
Region: residues 293	to 365
Annotation: disorder (Structural state)
Evidence: small-angle neutron scattering evidence used in manual assertion
Supporting statements:
The disorder in CD44ct is also exhibited in the SANS data. The relatively large Rg and Dmax of the 72-residue dCD44ct as compared with a well folded theoredoxin of 109 residues indicate that dCD44ct is not a compact globular structure (Fig. 1G and Table 1).
Protein: DP03806 (UniProt Q3U8S1)
Region: residues 293	to 365
Annotation: protein binding (Molecular function)
Evidence: gel-filtration evidence used in manual assertion
Supporting statements:
The gel filtration results show that CD44ct does not interact with Ezrin(T567D) in solution but forms a complex with Ezrin(T567D) only in the presence of PIP2 (Fig. 3A).
Protein: DP03806 (UniProt Q3U8S1)
Region: residues 293	to 365
Annotation: protein binding (Molecular function)
Evidence: glutathione S-transferase pull-down assay evidence used in manual assertion
Supporting statements:
Instead, only in the presence of PIP2, do CD44ct and FERM form a complex, as shown by gel filtration and pulldown experiments (Fig. 3, C and D).
Protein: DP03807 (UniProt A8K2U0)
Region: residues 634	to 668
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 634–668 in A2ML1’s LNK region could not be modeled, suggesting that this region adopts multiple conformations.
Cross-references: PDB:7Q1yY
Protein: DP03807 (UniProt A8K2U0)
Region: residues 696	to 726
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In both the EM and the X-ray structures of native A2ML1, it is not possible to model residues His696-Asp726, suggesting substantial flexibility of the intact bait region in accordance with its accessibility toward proteases (Fig. 1E, F).
Cross-references: PDB:7Q1yY
Protein: DP03809 (UniProt B6VDJ7)
Region: residues 50	to 65
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Missing residues in X-ray diffraction pattern interpretation.
Cross-references: PDB:5FC8
Protein: DP03810 (UniProt P0AFI0)
Region: residues 552	to 564
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
For most of the polypeptide chains, the electron density is well defined, excluding residues 1–4 and 551–564 (555–564 for the ADP complex) in both chains.
However, four additional amino acid residues at the C-terminus were pinpointed in the presence of the activator ADP that are not defined in the absence of this ligand.
In both enzyme species, the C-terminal part of the subunits is not involved in crystal packing contacts.
Residues 552-564 are disordered in all structures in the absence of ADP.
Cross-references: PDB:2Q27
PDB:2Q28
PDB:2Q29
Protein: DP03811 (UniProt Q00266)
Region: residues 1	to 13
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The first region is the N-terminal region Met1–Glu15, which has been found to be missing in most reported MAT structures owing to its flexibility.
Chain B contains three invisible regions, the N-terminus (Met1–Glu15), the gating loop (Asp116–Glu127) and the Phe250–Gly257 region, while chain A contains an ordered gating loop and the Phe250–Gly257 region shows a clear electron-density map.
Region 1-13 is disordered in all structures.
Cross-references: PDB:6SW5
PDB:6SW6
Protein: DP03812 (UniProt P33371)
Region: residues 99	to 111
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Owing to poor electron density, the regions Pro99–Thr111, Lys261–Tyr268, Lys297–Asn299 and Leu315–His322 were not modelled.
In the structure of EcoDusC, the adjacent loop above the active site (Pro99–Thr111) was disordered instead of this loop, suggesting that a different loop is used for tRNA recognition in TthDus and EcoDusC.
Cross-references: PDB:3W9Z
Protein: DP03813 (UniProt P0A6B7)
Region: residues 393	to 404
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The refined model consists of 385 residues/monomer (of 404 residues total) with residues 328–333 and 393–404 omitted due to poor electron density in these regions.
Cross-references: PDB:1P3W
Protein: DP03814 (UniProt Q9BU02)
Region: residues 215	to 230
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
A few residues are not sufficiently defined at the N and C terminal ends as well as in the loop connecting β6 and β7. In monomer A, residues 4 to 132 and 140 to 214 could be built in the electronic density while residues 5 to 132 and 141 to 211 of monomer B are present in the model.
Cross-references: PDB:3TVL
Protein: DP03815 (UniProt P32449)
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:
For all eight monomers, no electron density was found for residues M1 to D22.
The N-terminal region, found to be unstructured in both crystals of the E. coli and the yeast enzyme, was shown to become structured after the binding of an effector molecule and forming a lid supporting the coordination of the effector (26).
Cross-references: PDB:1HFB
Protein: DP03815 (UniProt P32449)
Region: residues 1	to 20
Annotation: positive regulation of catalytic activity (Biological process)
Evidence: deletion mutation phenotypic evidence used in manual assertion
Supporting statements:
Stable deletion of the N-terminal 20 amino acids resulted in an unregulated DAHP synthase with lowered activity in comparison to WT (11%).
Protein: DP03816 (UniProt Q99986)
Region: residues 1	to 20
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
The N-terminal tail (residues 1–20) is unstructured in solution as evidenced by the lack of medium and long range nuclear Overhauser effects (NOEs) in this region.
Cross-references: BMRB:16738
PDB:2LAV
Protein: DP03816 (UniProt Q99986)
Region: residues 343	to 364
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows the protein lacks electron density in this region, indicating it is disordered.
Cross-references: PDB:6AC9
Protein: DP03816 (UniProt Q99986)
Region: residues 342	to 353
Annotation: kinase activity (Molecular function)
Evidence: in vitro protein kinase assay evidence used in manual assertion
Supporting statements:
Our data showed that S342A and T353A mutants reduce the autocatalytic activities of VRK1, indicating that those residues play key roles in the kinase activity (supplemental Fig. S3).
Protein: DP03816 (UniProt Q99986)
Region: residues 342	to 364
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Nevertheless, the most complete polypeptide chain in this model contains an intact P-loop (chain A, residues 22–341; used for the structural comparisons below).
The PDB shows the protein lacks electron density in this region, indicating it is disordered.
Cross-references: PDB:5UVF
PDB:3OP5
PDB:5UKF
Protein: DP03817 (UniProt P42658)
Region: residues 117	to 126
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The first ten and last 16 residues of the extracellular domain of DPPX were disordered.
Cross-references: PDB:1XFD
Protein: DP03817 (UniProt P42658)
Region: residues 850	to 865
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The first ten and last 16 residues of the extracellular domain of DPPX were disordered.
Cross-references: PDB:1XFD
Protein: DP03818 (UniProt P57104)
Region: residues 1	to 13
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In an aqueous solution, temporin L adopts a random coil conformation, revealed by the single minimum at 200 nm (Fig.1).
Protein: DP03818 (UniProt P57104)
Region: residues 1	to 13
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
However, in the presence of small unilamellar vesicles, the peptide is α-helical, with the characteristic double minima at 210 and 222 nm. Compared with the zwitterionic SOPC small unilamellar vesicles, the helical conformation is more pronounced in the presence of the negatively charged phospholipid POPG, with the calculated helical content increasing from 69 to 89% at X POPG = 0 and 0.4, respectively.
Protein: DP03818 (UniProt P57104)
Region: residues 1	to 13
Annotation: lipid binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
However, in the presence of small unilamellar vesicles, the peptide is α-helical, with the characteristic double minima at 210 and 222 nm.