LiteFold/DisProt huggingface dataset:
Protein: DP04058 (UniProt Q9R0M6)
Region: residues 178	to 199
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The C-terminal
hypervariable region of Rab9A is disordered
and thus not required for RUTBC2 binding.
Residues 6–177 of Rab9A are well defined and
the C-terminal hypervariable region (residues 178–199) is disordered.
Cross-references: PDB:4QXA
Protein: DP04059 (UniProt Q8BXA0)
Region: residues 216	to 233
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
It starts with an unusual large insertion, disordered
in the crystal structure (Gln216-Phe233) before the last
β-strand of the extended LRR domain β-sheet; the first ordered residue
is Ala234 (marked in Fig. 1).
Cross-references: PDB:6F2O
Protein: DP04060 (UniProt Q8LGG8)
Region: residues 56	to 65
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Loops
comprising residues 56–65 and 137–145 are missing in all
the chains in the asymmetric unit, suggesting that these are
highly flexible regions.
Cross-references: PDB:2GM3
Protein: DP04061 (UniProt P29617)
Region: residues 1614	to 1626
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
A disordered region from residues 1314–1326 is not delineated.
The experimental electron density for residues 1245–1396 was readily traceable despite absent density for the disordered loop residues 1314–1326.
Cross-references: PDB:1MIJ
Protein: DP04062 (UniProt Q9Y4B6)
Region: residues 1486	to 1499
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The two beta-strands of DCAF1-FBD are
well defined, whereas the loop connecting the hairpin is completely
disordered (Fig. 2, A and B).
Cross-references: PDB:4P7I
Protein: DP04063 (UniProt P07275)
Region: residues 524	to 546
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Electron density for the 23-residue aldehyde substrate-binding loop is absent, implying substantial conformational flexibility in solution. We furthermore report a new crystal form of human ALDH4A1 (42% identical to Put2p) that also shows disorder in this loop.
The most conspicuous feature of the Put2p structure is that which is unseen. ALDHs have an ∼25-residue peptide that connects the last strand of the catalytic domain to the second piece of the oligomerization domain. This section corresponds to residues 523–547 of Put2p. Electron density for these residues is very weak, implying substantial conformational disorder (Figure ​3A).
Cross-references: PDB:4OE6
Protein: DP04063 (UniProt P07275)
Region: residues 23	to 42
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:4OE6
Protein: DP04063 (UniProt P07275)
Region: residues 379	to 390
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:4OE6
Protein: DP04063 (UniProt P07275)
Region: residues 566	to 575
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:4OE6
Protein: DP04063 (UniProt P07275)
Region: residues 379	to 395
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:4OE4
Protein: DP04064 (UniProt Q62765-2)
Region: residues 548	to 562
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Inspection of the electron density maps revealed weak electron density for the following loops: NL1 577–591, NL1 637–642, NL1 445–450, Nrx1β 289–291.
The region 577-591 that the authors mention corresponds to the 548-562 region of the Isoform 2 of Neuroligin-1 that was assessed.
Cross-references: PDB:3BIW
Protein: DP04064 (UniProt Q62765-2)
Region: residues 548	to 562
Annotation: order to disorder (Structural transition)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Inspection of the electron density maps revealed weak electron density for the following loops: NL1 577–591, NL1 637–642, NL1 445–450, Nrx1β 289–291.
The region 577-591 that the authors mention corresponds to the 548-562 region of the Isoform 2 of Neuroligin-1 that was assessed.
PDB structures show this region is disordered when forming a complex with  Neurexin-1, but ordered when the proteins is in solution.
Cross-references: PDB:3BIW
PDB:3BIX
Protein: DP04064 (UniProt Q62765-2)
Region: residues 548	to 562
Annotation: order (Structural state)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
PDB structures show this region is disordered when forming a complex with Neurexin-1, but ordered when the proteins is in solution.
Cross-references: PDB:3BIX
Protein: DP04065 (UniProt P38319)
Region: residues 1	to 67
Annotation: disorder (Structural state)
Evidence: in vitro cleavage assay evidence used in manual assertion
Supporting statements:
During crystallization trials of full-length yTdp1, protein degradation was observed from the N terminus, but limited trypsin digestion revealed that the N-terminal 67 residues could be removed to generate a stable molecule.
Protein: DP04065 (UniProt P38319)
Region: residues 68	to 78
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The structure revealed that 11 and five additional residues could be removed from the N terminus and the C terminus, respectively, and Tdp1-Δ2 yielded superior crystals that generated the final 2.0 Å structure.
The crystal structure of an equivalent fragment of human Tdp1 allowed some missing segments to be added,25 but we were unable to locate any electron density for N-terminal residues 68–78 or Cterminal residues 540–544.
Cross-references: PDB:1Q32
Protein: DP04065 (UniProt P38319)
Region: residues 342	to 352
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
All four molecules contain five peripheral regions that are not visible in the electron density map and are presumably disordered (Figure 1(a) and (b)).
Residues 342-352 are missing in all chains and are presumably disordered.
Cross-references: PDB:1Q32
Protein: DP04066 (UniProt P0A8P8)
Region: residues 101	to 110
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The missing residues are located at the N- and C-termini and in three disordered surface loops.
Residues that are not defined are located at the N- and C-termini and in three disordered loops (residues 64–70, 101–110 and 269–270).
Cross-references: PDB:1A0P
Protein: DP04066 (UniProt P0A8P8)
Region: residues 101	to 110
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The enzyme comprises two domains: domain 1 consists of residues 1–107, while domain 2 comprises residues 108–298 (Figure 1).
Based on the structure, loop 101-110 is a flexible linker region between the two domains of the protein.
Cross-references: PDB:1A0P
Protein: DP04067 (UniProt Q9H078)
Region: residues 208	to 227
Annotation: disorder (Structural state)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The long β-hairpin of Ank2 is labeled with the disordered regions flanking helix α5 (brown) indicated by dashed lines. 
Cross-references: PDB:8DEH
Protein: DP04068 (UniProt P19632)
Region: residues 36	to 67
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues P35–P65 of phosducin are largely disordered and do not make contact with the top of the β propeller of Gtβ. Instead, residues in this loop make contact with a symmetry-related molecule (1/2–x,1–y,1/2+z).
Cross-references: PDB:1A0R
Protein: DP04068 (UniProt P19632)
Region: residues 1	to 12
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues not in bold type have poor electron density in phosducin (and may be quite mobile parts of the structure), or are regions in the rat phosducin-like protein and the two yeast phosducin-like proteins that are likely to have a different structure to that observed in phosducin.
Protein: DP04068 (UniProt P19632)
Region: residues 231	to 245
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues not in bold type have poor electron density in phosducin (and may be quite mobile parts of the structure), or are regions in the rat phosducin-like protein and the two yeast phosducin-like proteins that are likely to have a different structure to that observed in phosducin.
Cross-references: PDB:1A0R
Protein: DP04070 (UniProt Q96F81)
Region: residues 254	to 291
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
On the other hand, the loop between residues 253–292, which is absent in both PTCH1 and NPC1, is disordered in the map (Fig 2B and C), indicating that the flexibility of this large loop permits it to be accessible to Furin and the cleavage by Furin may release this internal loop to facilitate the endosomal trafficking of DISP1 (Stewart et al, 2018).
Cross-references: PDB:6XE6
Protein: DP04070 (UniProt Q96F81)
Region: residues 254	to 291
Annotation: flexible linker (Disorder function)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
On the other hand, the loop between residues 253–292, which is absent in both PTCH1 and NPC1, is disordered in the map (Fig 2B and C), indicating that the flexibility of this large loop permits it to be accessible to Furin and the cleavage by Furin may release this internal loop to facilitate the endosomal trafficking of DISP1 (Stewart et al, 2018).
Cross-references: PDB:6XE6
Protein: DP04070 (UniProt Q96F81)
Region: residues 390	to 414
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The densities of residues 172–178, 253–294, 306–312, 337–347, 390–414, 442–446, 477–484, 663–687, 771–777, 866–871, 897–902, and 1,145–1,249 were not resolved nor built.
Cross-references: PDB:6XE6
Protein: DP04070 (UniProt Q96F81)
Region: residues 663	to 687
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The densities of residues 172–178, 253–294, 306–312, 337–347, 390–414, 442–446, 477–484, 663–687, 771–777, 866–871, 897–902, and 1,145–1,249 were not resolved nor built.
Cross-references: PDB:6XE6
Protein: DP04070 (UniProt Q96F81)
Region: residues 1145	to 1249
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The densities of residues 172–178, 253–294, 306–312, 337–347, 390–414, 442–446, 477–484, 663–687, 771–777, 866–871, 897–902, and 1,145–1,249 were not resolved nor built.
Cross-references: PDB:6XE6
Protein: DP04070 (UniProt Q96F81)
Region: residues 1	to 180
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
An N-terminal cytoplasmic segment consisting of 180 amino acid residues preceding TM1, and the C-terminal cytoplasmic segment consisting of 380 residues following TM12 were not resolved in either cryo-EM density map (Fig. 2c and Supplementary Fig. 4c), likely due to their intrinsic flexibility.
Cross-references: PDB:7E2I
Protein: DP04070 (UniProt Q96F81)
Region: residues 1149	to 1524
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
An N-terminal cytoplasmic segment consisting of 180 amino acid residues preceding TM1, and the C-terminal cytoplasmic segment consisting of 380 residues following TM12 were not resolved in either cryo-EM density map (Fig. 2c and Supplementary Fig. 4c), likely due to their intrinsic flexibility.
Cross-references: PDB:7E2I
Protein: DP04070 (UniProt Q96F81)
Region: residues 263	to 280
Annotation: limited proteolysis display site (Disorder function)
Evidence: qualitative western immunoblotting evidence used in manual assertion
Supporting statements:
Purified hDisp1NNN migrated on SDS-PAGE as two larger bands with apparent molecular weights of ~175 and ~145kDa, and two smaller bands with apparent molecular weights of ~35 and ~30kDa (Fig. 1b, left panel). Western blotting indicated that the 175kDa band corresponds to FL hDisp1NNN, as it contained both the N-terminal Flag tag and C-terminal His tag, the 145kDa band corresponds to a cleaved product with only the C-terminal His tag (hDisp1NNN-C145), while the two smaller bands correspond to cleaved products with only the N-terminal Flag tag (hDisp1NNN-N35 and hDisp1NNN-N30) (Fig. 1b, right panel). This cleavage pattern of hDisp1NNN is consistent with the recently reported partial cleavage of mouse and Drosophila Disp proteins by Furin protease31.
Protein: DP04070 (UniProt Q96F81)
Region: residues 1	to 180
Annotation: flexible N-terminal tail (Disorder function)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Disp homologues contain 12 transmembrane segments (TMs), two large extracellular domains (ECD1 and ECD2), as well as flexible N- and C-terminal intracellular domains.
Cross-references: PDB:7E2I
Protein: DP04070 (UniProt Q96F81)
Region: residues 1145	to 1524
Annotation: flexible C-terminal tail (Disorder function)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Disp homologues contain 12 transmembrane segments (TMs), two large extracellular domains (ECD1 and ECD2), as well as flexible N- and C-terminal intracellular domains.
Cross-references: PDB:7E2I
Protein: DP04070 (UniProt Q96F81)
Region: residues 662	to 686
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-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:7E2I
Protein: DP04070 (UniProt Q96F81)
Region: residues 263	to 285
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
A connecting loop between residues 263–285 in ECD1 (named the C-loop, for protease cleavage) is not well-resolved in our reconstruction, indicating its flexibility; we speculate that this permits its accessibility to Furin or 3C protease cleavage (Fig. 2b). While the absence of density for the C-loop creates the appearance of a large cavity between the two ECDs (Fig. 2a, b), it is important to emphasize that the C-loop, though unstructured, still occupies this space in uncleaved hDisp1NNN-3C (see below).
Cross-references: PDB:7E2I
Protein: DP04070 (UniProt Q96F81)
Region: residues 263	to 285
Annotation: flexible linker (Disorder function)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
A connecting loop between residues 263–285 in ECD1 (named the C-loop, for protease cleavage) is not well-resolved in our reconstruction, indicating its flexibility; we speculate that this permits its accessibility to Furin or 3C protease cleavage (Fig. 2b). While the absence of density for the C-loop creates the appearance of a large cavity between the two ECDs (Fig. 2a, b), it is important to emphasize that the C-loop, though unstructured, still occupies this space in uncleaved hDisp1NNN-3C (see below).
Cross-references: PDB:7E2I
Protein: DP04070 (UniProt Q96F81)
Region: residues 263	to 280
Annotation: limited proteolysis display site (Disorder function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
To this end, we replaced the region in hDisp1 recognized by Furin (residues 263–280) with a cleavage site for the highly specific 3C protease (Fig. 1c), and we purified to homogeneity the resulting hDisp1NNN-3C protein (Supplementary Fig. 1c). Purified hDisp1NNN-3C migrated as a single band on SDS-PAGE, of the same molecular weight as FL hDisp1NNN (Fig. 1d). Notably, the hDisp1NNN-3C preparation was devoid of the low molecular weight species found in purified hDisp1NNN (Fig. 1d), indicating that Furin cleavage had been successfully abolished.
Protein: DP04072 (UniProt Q12402)
Region: residues 79	to 88
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
As expected, the amide cross-peaks of the N- and C-terminal residues, the loop between TM1 and TM2 (comprising the GGVG motif), the flexible region connecting TM2 and TM3, and the region connecting the C-terminal end of TM4 and the APH were broadened, indicating exposure to the water-soluble Mn+2EDDA (Fig. 3B).
Compared with the C terminus, the next most flexible region is the region of the 10-residue loop connecting TM2 to TM3.
In Figure 3 authors state residues 79-88 constitute a linker region
Protein: DP04072 (UniProt Q12402)
Region: residues 79	to 88
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
As expected, the amide cross-peaks of the N- and C-terminal residues, the loop between TM1 and TM2 (comprising the GGVG motif), the flexible region connecting TM2 and TM3, and the region connecting the C-terminal end of TM4 and the APH were broadened, indicating exposure to the water-soluble Mn+2EDDA (Fig. 3B)
Compared with the C terminus, the next most flexible region is the region of the 10-residue loop connecting TM2 to TM3.
In Figure 3 authors state residues 79-88 constitute a linker region.
Protein: DP04073 (UniProt P63103)
Region: residues 204	to 215
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The disordered loop formed by residues 203 to 216 is shown schematically as a thin ribbon.
Cross-references: PDB:1A4O
Protein: DP04073 (UniProt P63103)
Region: residues 229	to 245
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Surface-charge representation of a monomer of 14-3-3 calculated with the program GRASP21 , after removal of the C-terminal loop (231 to 245).
Cross-references: PDB:1A4O
Protein: DP04073 (UniProt P63103)
Region: residues 229	to 245
Annotation: flexible C-terminal tail (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Surface-charge representation of a monomer of 14-3-3 calculated with the program GRASP21 , after removal of the C-terminal loop (231 to 245).
Cross-references: PDB:1A4O
Protein: DP04074 (UniProt Q9Y6X9)
Region: residues 551	to 603
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
We did not observe electron density for the second predicted coiled coil, CC2 (residues 551–603).
Cross-references: PDB:5OF9
Protein: DP04075 (UniProt Q9Y2M5)
Region: residues 303	to 316
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The structure was refined at 1.1-Å resolution and traced the full KLHL20 Kelch domain from residues 317 to 601 (Figure 3A).
Cross-references: PDB:6GY5
Protein: DP04076 (UniProt P35790)
Region: residues 151	to 173
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the ΔN-ChoKα1 ternary complex, for instance, the region flanking the segment (residues 155–172), which is missing in ChoKα2 due to alternative splicing (Fig. 1), was invisible in our maps.
Cross-references: PDB:3G15
Protein: DP04077 (UniProt Q9UQ13)
Region: residues 1	to 85
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
High-resolution x-ray crystal structures of this region from other PP1C binding partners overlay well with this density (Extended Data Fig. 6d–f), whereas the rest of the SHOC2 N terminus (residues 1–85) was disordered (Extended Data Figs. 3e and 5d).
Cross-references: PDB:7SD1
Protein: DP04077 (UniProt Q9UQ13)
Region: residues 1	to 85
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
All proteins show an extended tail at high r values indicative of the unfolded SHOC2 N terminus.
Protein: DP04078 (UniProt P35790-2)
Region: residues 50	to 81
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-terminal 30 amino acids (residues 49–80) of our construct are not visible in the electron density maps of all three structures, indicating that they are disordered in the crystals.
Cross-references: PDB:2CKQ
Protein: DP04078 (UniProt P35790-2)
Region: residues 50	to 85
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-terminal 30 amino acids (residues 49–80) of our construct are not visible in the electron density maps of all three structures, indicating that they are disordered in the crystals.
Cross-references: PDB:2CKO
PDB:2CKP