LiteFold/DisProt huggingface dataset:
Protein: DP02490 (UniProt D1A4G7)
Region: residues 200	to 413
Annotation: localization (Biological process)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Although the full protein is present in the crystal (Figure S3C), the N-terminal “DUF” domain and linker1 are disordered in the structure and could not be modeled
The DUF domain, which is required for secretion in vivo
Cross-references: PDB:4NH0
PDB:4N1A
Protein: DP02491 (UniProt Q9WBP8)
Region: residues 1	to 216
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
As reported for other AAV structures, the VP was ordered from residue 217 within the VP3 common region, with the VP1u and VP1/2 common regions being disordered
Protein: DP02491 (UniProt Q9WBP8)
Region: residues 127	to 131
Annotation: transduction (Biological process)
Evidence: author statement used in manual assertion
Supporting statements:
Residues 129, 418, and 642 have been reported to play a role in AAV1 and AAV6 transduction (62, 63). Residue 129 is not ordered in the AAV structures, while T502 is at a distance of 38.9 and 35.4 Å from 418 and 642, respectively, located on the interior surface of the capsid. 
Annotation pertaining residue Leu129.
Protein: DP02492 (UniProt Q808Y3)
Region: residues 1	to 216
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Amino acid residues 1–217, which includes the VP1u (1–137), the VP1/2 common region (138–202), and the first 15 N-terminal residues of VP3 are disordered in the density maps.
Cross-references: PDB:4RSO
Protein: DP02493 (UniProt P21401)
Region: residues 154	to 370
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Interestingly, only residues constituting domain B were resolved in our crystallographic dataset (residue numbers 370–379 and 397–437). Electron density corresponding to both domain A and the β-ribbon domain of RVFV Gn was not visible and could not be sterically accommodated in the RVFV Gn-Fab RV-Gn1 crystal, indicating that these regions were likely cleaved during crystallogenesis
Previous structural analyses of RVFV Gn have revealed a triangular organization composed of three domains: domain A (residues 154–300), domain B (residues 366–439), and a β-ribbon domain (residues 301–365 and 440–469)
Cross-references: PDB:6I9I
Protein: DP02493 (UniProt P21401)
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:
Interestingly, only residues constituting domain B were resolved in our crystallographic dataset (residue numbers 370–379 and 397–437). Electron density corresponding to both domain A and the β-ribbon domain of RVFV Gn was not visible and could not be sterically accommodated in the RVFV Gn-Fab RV-Gn1 crystal, indicating that these regions were likely cleaved during crystallogenesis
Previous structural analyses of RVFV Gn have revealed a triangular organization composed of three domains: domain A (residues 154–300), domain B (residues 366–439), and a β-ribbon domain (residues 301–365 and 440–469)
Cross-references: PDB:6I9I
Protein: DP02493 (UniProt P21401)
Region: residues 440	to 469
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Interestingly, only residues constituting domain B were resolved in our crystallographic dataset (residue numbers 370–379 and 397–437). Electron density corresponding to both domain A and the β-ribbon domain of RVFV Gn was not visible and could not be sterically accommodated in the RVFV Gn-Fab RV-Gn1 crystal, indicating that these regions were likely cleaved during crystallogenesis
Previous structural analyses of RVFV Gn have revealed a triangular organization composed of three domains: domain A (residues 154–300), domain B (residues 366–439), and a β-ribbon domain (residues 301–365 and 440–469)
Cross-references: PDB:6I9I
Protein: DP02494 (UniProt O56139)
Region: residues 1	to 216
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The AAV-3B model contains amino acids 217 to 734 (VP1 numbering)
Interpretable density starts at VP3 residue 15 (residue 217 in the conventional VP1 numbering).
Cross-references: PDB:3KIC
PDB:3KIE
Protein: DP02495 (UniProt Q928V6)
Region: residues 133	to 350
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
We also analyzed the oligomeric properties of the isolated CC domain (residues 345–405). Despite the absence of the remainder of the CTD into which the CC is embedded, the isolated CC polypeptide is soluble and forms stable dimers at >300 μM concentration
The carboxy-terminal domain (CTD) corresponds to region 133-452.
Cross-references: PDB:5UDO
Protein: DP02495 (UniProt Q928V6)
Region: residues 400	to 452
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
We also analyzed the oligomeric properties of the isolated CC domain (residues 345–405). Despite the absence of the remainder of the CTD into which the CC is embedded, the isolated CC polypeptide is soluble and forms stable dimers at >300 μM concentration
The carboxy-terminal domain (CTD) corresponds to region 133-452.
Cross-references: PDB:5UDO
Protein: DP02496 (UniProt P56926)
Region: residues 633	to 852
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The structural organization of Dr GlnRS was established by separate multiple sequence alignments. A first alignment of known bacterial GlnRSs shows that Dr GlnRS is highly similar to other bacterial GlnRSs, with the exception of a few insertions (17, 27 and 5 additional residues in the structured region 410–433 and in two loops 535–565 and 610–620, respectively) and the presence of a short N-terminal extension (M1–A43) and a long C-terminal appendix (G633–A862)
Cross-references: PDB:2HZ7
Protein: DP02496 (UniProt P56926)
Region: residues 633	to 852
Annotation: tRNA binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The structural organization of Dr GlnRS was established by separate multiple sequence alignments. A first alignment of known bacterial GlnRSs shows that Dr GlnRS is highly similar to other bacterial GlnRSs, with the exception of a few insertions (17, 27 and 5 additional residues in the structured region 410–433 and in two loops 535–565 and 610–620, respectively) and the presence of a short N-terminal extension (M1–A43) and a long C-terminal appendix (G633–A862)
Kinetic investigations and tRNA-binding experiments of full length and Yqey-truncated GlnRSs reveal that the Yqey domain is involved in tRNAGln recognition.
Remarkably, the Yqey domain has a disordered orientation in the structure of GlnRS where it acts as a tRNAGln affinity enhancer.
Cross-references: PDB:2HZ7
Protein: DP02496 (UniProt P56926)
Region: residues 633	to 852
Annotation: molecular function regulator (Molecular function)
Evidence: enzymatic activity assay evidence used in manual assertion
Supporting statements:
Remarkably, the Yqey domain has a disordered orientation in the structure of GlnRS where it acts as a tRNAGln affinity enhancer.
Taken together, the Yqey flexible module increases the catalytic efficiency of GlnRS for both tRNAGln-dependent Gln activation and tRNAGln charging and is involved in binding of tRNAGln to GlnRS.
Cross-references: PDB:2HZ7
Protein: DP02498 (UniProt A7YK37)
Region: residues 1	to 227
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Similar to the apo CW1 murine norovirus P domain structure (PDB code 3LQ6), the CR10 P domain could be divided into P1-1 (residues 228 to 277), P2 (residues 278 to 416), and P1-2 (residues 417 to 530) subdomains.
No density is visible for residues 1-227 of the capsid protein
Cross-references: PDB:5OR7
Protein: DP02499 (UniProt A0KJC7)
Region: residues 1	to 230
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The structure of an Ah TssA2A Nt2 domain construct (D231-L374) was solved to 1.76 Å with four subunits (chains A–D) in the asymmetric unit
Cross-references: PDB:6G7B
Protein: DP02500 (UniProt Q5A3P6)
Region: residues 1	to 232
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Later, crystal structure analysis revealed that one molecule of the catalytic domain (aa 233-521, 33.4 kDa) crystallized per asymmetric unit, corresponding to a V M of 2.26 Å 3 /Da and a solvent content of 46% (v/v).
Cross-references: PDB:4C0T
Protein: DP02500 (UniProt Q5A3P6)
Region: residues 522	to 944
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Later, crystal structure analysis revealed that one molecule of the catalytic domain (aa 233-521, 33.4 kDa) crystallized per asymmetric unit, corresponding to a V M of 2.26 Å 3 /Da and a solvent content of 46% (v/v).
Cross-references: PDB:4C0T
Protein: DP02501 (UniProt P00800)
Region: residues 1	to 232
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
No density is visible for residues 1–232 of Thermolysin
Cross-references: PDB:5A3Y
Protein: DP02502 (UniProt A0R1T8)
Region: residues 1	to 238
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Several proteolysis sites could result in this 6 kDa fragment. For example, 3C protease was used to remove the N-terminal affinity tag, and aberrant cleavage could have occurred at residue Gln237. Alternatively, cleavage could have occurred at Arg238 by the trypsin-like protease II of E. coli (Strongin et al., 1979 ▸) if this protease were retained in tiny amounts after purification.
N-terminal to the first ordered residue of the dimerization domain is a short linker at residue Arg238 followed by the last α-helix of the GTPase domain, via analogy to other family members. As described above, Gln237 and Arg238 are possible proteolytic sites for the fragment crystallized here.
Cross-references: PDB:6CUM
Protein: DP02502 (UniProt A0R1T8)
Region: residues 1	to 238
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Several proteolysis sites could result in this 6 kDa fragment. For example, 3C protease was used to remove the N-terminal affinity tag, and aberrant cleavage could have occurred at residue Gln237. Alternatively, cleavage could have occurred at Arg238 by the trypsin-like protease II of E. coli (Strongin et al., 1979 ▸) if this protease were retained in tiny amounts after purification.
N-terminal to the first ordered residue of the dimerization domain is a short linker at residue Arg238 followed by the last α-helix of the GTPase domain, via analogy to other family members. As described above, Gln237 and Arg238 are possible proteolytic sites for the fragment crystallized here.
Cross-references: PDB:6CUM
Protein: DP02503 (UniProt Q28146)
Region: residues 31	to 280
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The L-shaped molecule can be divided into a flexible repeat I (LNS1-EGF-A-LNS2), a rigid horseshoe-shaped repeat II (LNS3-EGF-B-LNS4) with structural similarity to so-called reelin repeats, and an extended repeat III (LNS5-EGF-B-LNS6) with controlled flexibility.
Neurexin repeat I is flexible
No electron density is observed for L1 and EGF-A, though present in the crystal, suggesting that these N-terminal modules are disordered and can adopt multiple conformations. Thus, the crystal structure of n1α reveals 7 out of 9 modules (1003 residues per molecule) organized in an L-shaped assembly.
N1α appears increasingly flexible towards its N-terminus
The L1-EGF-A-L2 repeat appears flexible, as L1 and EGF-A are not visible in the crystal structure.
Continuous electron density is visible for L2, L3, EGF-B, L4, L5, EGF-C and L6 (residues Glu281-Val1337), including interconnecting residues.
Cross-references: PDB:3QCW
PDB:3R05
Protein: DP02504 (UniProt P35828)
Region: residues 1	to 248
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-terminal region of RsaA is a putative LPS binding region (see Figure S2), residues 249-1026 are resolved in the X-ray structure
RsaA amino acid residues 249-1026 were resolved in the resulting electron density map
Cross-references: PDB:5N8P
Protein: DP02504 (UniProt P35828)
Region: residues 1	to 256
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
At least amino acid residues 256-1026 were still present in the crystallised protein as determined by mass spectrometry after protease cleavage into peptides, a method that does not reveal the exact N- and C-termini of the analysed polypeptide
Cross-references: PDB:5N8P
Protein: DP02505 (UniProt O53168)
Region: residues 1	to 262
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In a previous study, we determined the crystal structure of a self-inactivated form of RipA in which the catalytic site cleft of the enzyme is physically locked by a pro-domain, and proposed that the activation of the RipA zymogen occurs through proteolytic cleavage (Ruggiero, Marasco et al., 2010). Recent work has confirmed that RipA is proteolytically activated in vivo and that overproduction of activated RipA produces severe growth defects in Mtb (Chao et al., 2013).
Cross-references: PDB:4Q4G
PDB:4Q4T
PDB:4Q4N
Protein: DP02506 (UniProt Q8A6W3)
Region: residues 1	to 235
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Region 1-235 is not visible in the crystal structure of SusC homolog
A dataset to 3.1 Å resolution collected on this crystal at DLS beamline I04 generated a definite MR solution with Phaser (RFZ=6.8 TFZ=14.4 PAK=0 LLG=173 TFZ==14.7 RFZ=7.0 TFZ=7.6 PAK=9 LLG=627 TFZ==10.4 LLG=807 TFZ==10.0; space group P21212), using the BT1762 structure and a Sculptor-generated model of BT2264 (21% sequence identity) as search models. In this crystal, there is only one SusC protomer within the asymmetric unit, with the SusC homodimer generated by crystallographic symmetry.
Cross-references: PDB:5T3R
Protein: DP02507 (UniProt Q84852)
Region: residues 17	to 299
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The 282 residues N-terminal to the PRCV RBD in the S3H protein were largely disordered or degraded during crystallization, and are absent in the structure.
Cross-references: PDB:4F5C
Protein: DP02508 (UniProt P12537)
Region: residues 304	to 585
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The ordered region of IIIa (aa 1–300) is composed of mostly α-helices and organized as two domains: NT domain (NTD; aa 1–134) and middle domain (MDLD; aa 135–300) (Fig. 3c). The CT domain (CTD; aa 400–585), which also contains a few (predicted) helices, is disordered.
From Table 2, 1–303 corresponds to the ordered region of IIIa and 304–585 corresponds to the disordered region of IIIa. Also the PDB show this boundaries as disordered (304-585).
Cross-references: PDB:6CGV
EMDB:7034
Protein: DP02509 (UniProt P0DOC6)
Region: residues 103	to 174
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the LshC2c2-crRNA binary structure, residues 103–174 within the NTD domain and residues 914–1005 within the Linker of LshC2c2 are disordered
The larger subdomain of NTD contains an ordered segment comprising seven α helices, as well as a disordered segment between residues 103–174.
Cross-references: PDB:5WTJ
PDB:5WTK
Protein: DP02509 (UniProt P0DOC6)
Region: residues 914	to 1005
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the LshC2c2-crRNA binary structure, residues 103–174 within the NTD domain and residues 914–1005 within the Linker of LshC2c2 are disordered
residues 914 to 1005 are disordered
Cross-references: PDB:5WTJ
PDB:5WTK
Protein: DP02509 (UniProt P0DOC6)
Region: residues 914	to 1005
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the LshC2c2-crRNA binary structure, residues 103–174 within the NTD domain and residues 914–1005 within the Linker of LshC2c2 are disordered
residues 914 to 1005 are disordered
the Linker connecting the HEPN1 and HEPN2 domains is partially disordered, in contrast to the ordered structure in the crRNA-free state (discussed further below). Those residues that are ordered in the crRNA-bound structure form eight α helices, while residues 914 to 1005 are disordered.
Cross-references: PDB:5WTJ
PDB:5WTK
Protein: DP02510 (UniProt P09327)
Region: residues 360	to 613
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
An unambiguous solution showed that the diffraction originated solely from V6, with the V4 and V5 domains and actin not evident.
Cross-references: PDB:3FG7
Protein: DP02511 (UniProt P02640)
Region: residues 723	to 763
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The isolated sixth gelsolin repeat and headpiece domain of villin bundle F-actin in the presence of calcium and are linked by a 40-residue unstructured sequence
D6-HP consists of two structured domains, D6 and HP, separated by an unfolded linker sequence
The linker sequence, positions 105-145, is characterized by the 1HN chemical shift values narrowly clustered between 8.0-8.5 ppm consistent with a random coil, unfolded polypeptide.
The 15N backbone relaxation rates R1 and R2 as well as the {1H-15N}-NOE (Figure 4 A,B,C) indicate three distinct structural entities within D6-HP, namely two structured regions, positions 1-105 and 145-206, and a disordered sequence in between.
Cross-references: BMRB:15097
Protein: DP02511 (UniProt P02640)
Region: residues 723	to 763
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The isolated sixth gelsolin repeat and headpiece domain of villin bundle F-actin in the presence of calcium and are linked by a 40-residue unstructured sequence
D6-HP consists of two structured domains, D6 and HP, separated by an unfolded linker sequence
The linker sequence, positions 105-145, is characterized by the 1HN chemical shift values narrowly clustered between 8.0-8.5 ppm consistent with a random coil, unfolded polypeptide.
The 15N backbone relaxation rates R1 and R2 as well as the {1H-15N}-NOE (Figure 4 A,B,C) indicate three distinct structural entities within D6-HP, namely two structured regions, positions 1-105 and 145-206, and a disordered sequence in between.
Cross-references: BMRB:15097
Protein: DP02513 (UniProt Q05022)
Region: residues 1	to 1408
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The density, although weak, was well fitted by the crystal structure of the C-terminal tetratricopeptide repeat (TPR) domain of Rrp5
Cross-references: PDB:5WYJ
Protein: DP02514 (UniProt P36594)
Region: residues 1498	to 1752
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The last ordered residue of S. cerevisiae Rpb1 was Leu-1450, whereas the S. pombe chain could be traced as far as residue 1497
Cross-references: PDB:3H0G
Protein: DP02515 (UniProt Q13740)
Region: residues 246	to 583
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
X-Ray diffraction data for crystals containing CD166 VVC were collected to 1.86 Å and the structure solved by molecular replacement with a search model derived from the second IgSF domain of RAGE (PDB: 3CJJ, 16.4% sequence identity to domain 1 and 30.3% to domain 2; Koch et al., 2010). Only the first two domains could be resolved in the electron density map (Figures 2C and 2D). The crystal lattice did not contain space to accommodate the third domain, suggesting it had been proteolytically cleaved prior to crystal growth.
Cross-references: PDB:5A2F
Protein: DP02516 (UniProt P56287)
Region: residues 443	to 678
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
the HEAT domains, whose electron densities were not observed in our structure
We determined the crystal structure of eIF2B at 3.0-Å resolution, and assigned almost all regions except for the ε-subunit HEAT domains
Cross-references: PDB:5B04
Protein: DP02516 (UniProt P56287)
Region: residues 443	to 678
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
missing residues in PDB. Article from the authors that previously identified this region in PMID:26901872
Cross-references: PDB:6JLY
PDB:6JLZ
Protein: DP02517 (UniProt Q64487-12)
Region: residues 585	to 854
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Electron density of the Fn4 domain and subsequent C-terminal region was not visible, likely due to the disorder
Cross-references: PDB:4yh7
Protein: DP02518 (UniProt Q8ZRW0)
Region: residues 1	to 224
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Mass spectrometry confirmed the N-terminal LptD 24–224 amino acids and LptE residues 170–196 were removed by α-chymotrypsin
Cross-references: PDB:4N4R