LiteFold/DisProt huggingface dataset:
Protein: DP03171 (UniProt Q16831)
Region: residues 1	to 15
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Due to a lack of electron-density, the first 15 residues of hUPP1 and the N-terminal cloning artifact residues 'MRGSHHHHHHGSPGLQEF' were not built.
Cross-references: PDB:3EUE
PDB:3EUF
Protein: DP03172 (UniProt Q9NRN7)
Region: residues 248	to 263
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Another feature is the disordered loop between residues 248–263, which starts after the superposition of the PPT C-terminal domain and AcpS ends, suggesting that this may act as a flexible linker.
Cross-references: PDB:2BYD
PDB:2C43
Protein: DP03173 (UniProt O14727)
Region: residues 1	to 100
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The disordered N-terminus of APAF contains the caspase recruitment domain (CARD).
The seven CARDs exhibit no EM density, likely reflecting their dynamic locations.
Cross-references: PDB:3JBT
EMDB:EMD-6480
Protein: DP03173 (UniProt O14727)
Region: residues 1	to 104
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The disordered N-terminus of APAF contains the caspase recruitment domain (CARD).
We surmise that the three excluded Apaf-1 CARDs are disordered since they are not visible, but they may contribute to the propensity of the particles to aggregate.
Cross-references: PDB:5JUY
EMDB:EMD-8178
Protein: DP03174 (UniProt Q3UKX1)
Region: residues 1	to 106
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-terminal module of mPRMT2 (residues 1-106)
partially folded in a SH3 domain is missing in the electron density although present in the crystal.
We reveal that the N-terminal containing SH3 module is
disordered in the full-length crystal structures, and highlight idiosyncratic features of the PRMT2
active site.
Therefore, unlike zPRMT2, the absence of residues 1–106 in the electron density map was not the result of proteolysis before or during the crystallization process, but could be explained by a high flexibility of the N-terminal region within the crystals.
Cross-references: PDB:5FUL
PDB:5FWD
PDB:5FWA
Protein: DP03175 (UniProt A1L1Q4)
Region: residues 1	to 71
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
 The electron density map revealed the absence of residues 1-71 corresponding to
the N-terminus part containing the SH3 domain.
Protein: DP03176 (UniProt Q10344)
Region: residues 40	to 61
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We have determined the three-dimensional structure of p23fyp, the TCTP from S. pombe, by heteronuclear NMR spectroscopy using a total of 2,254 experimentally determined restraints. Excluding the region Gly 40–Gly 61, which is highly mobile and disordered10, the structure is well defined (Fig. 2a; Table 1). 
Cross-references: PDB:1H7Y
PDB:1H6Q
Protein: DP03177 (UniProt Q8CJ26)
Region: residues 1	to 54
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
N-terminal ectodomain is 54 residues long (excl. N-terminal tag) and is disordered.
The unstructured nature of both N- and C-terminal juxta-membrane regions is supported by the lack of long-range NOEs and analysis of chemical shifts in TALOS-N software (see Figure 2B).
Cross-references: PDB:6HJ7
Protein: DP03177 (UniProt Q8CJ26)
Region: residues 78	to 127
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The cytoplasmic domain consists of two parts: an intrinsically disordered juxta-membrane region and a globular C-terminal death domain. The unstructured nature of both N- and C-terminal juxta-membrane regions is supported by the lack of long-range NOEs and analysis of chemical shifts in TALOS-N software (see Figure 2B).
Cross-references: PDB:6HJ7
Protein: DP03178 (UniProt Q99250)
Region: residues 1777	to 1789
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The ordered structure extends from residues Leu-1790 to Glu-1868 and is composed of
four α-helices separated by two short anti-parallel -strands; a less well defined helical region extends from residue Ser-1869 to Arg-1882, and a disordered N-terminal region encompasses residues 1777–1789.
The cis conformation is evidenced by stronger X-Pro Hα-Hα than X-Pro Hα-Hδ NOE contacts and differences of Cβ-Cγ chemical shifts of 9.4 and 8.5 ppm, respectively (59, 60).
Medium range 1 H-1 H NOEs, steady-state {1H}-15N NOE, and 13Cα secondary chemical shifts for NaV1.2 indicate that the CTD forms a well folded domain between residues Leu-1790
and Glu-1868, with a less well ordered region between residues Ser-1869 and Arg-1882 and a disordered N-terminal region between residues Gly-1777 and Pro-1789 (Fig. 1 and supplemental Fig. S1).
Cross-references: PDB:2KAV
Protein: DP03178 (UniProt Q99250)
Region: residues 1	to 116
Annotation: disorder (Structural state)
Evidence: electron microscopy evidence used in manual assertion
Supporting statements:
For Nav1.2, the N-terminal 116 residues, extracellular loop (residues 285-313), intracellular I-II linker (residues 442-739), II-III linker (residues 988-1190), and C-terminal sequences after Ser1786 were not modelled due to the lack of corresponding densities. 
Cross-references: PDB:6J8E
Protein: DP03178 (UniProt Q99250)
Region: residues 285	to 313
Annotation: disorder (Structural state)
Evidence: electron microscopy evidence used in manual assertion
Supporting statements:
For Nav1.2, the N-terminal 116 residues, extracellular loop (residues 285-313), intracellular I-II linker (residues 442-739), II-III linker (residues 988-1190), and C-terminal sequences after Ser1786 were not modelled due to the lack of corresponding densities. 
Cross-references: PDB:6J8E
Protein: DP03178 (UniProt Q99250)
Region: residues 442	to 739
Annotation: disorder (Structural state)
Evidence: electron microscopy evidence used in manual assertion
Supporting statements:
For Nav1.2, the N-terminal 116 residues, extracellular loop (residues 285-313), intracellular I-II linker (residues 442-739), II-III linker (residues 988-1190), and C-terminal sequences after Ser1786 were not modelled due to the lack of corresponding densities. 
Cross-references: PDB:6J8E
Protein: DP03178 (UniProt Q99250)
Region: residues 988	to 1190
Annotation: disorder (Structural state)
Evidence: electron microscopy evidence used in manual assertion
Supporting statements:
For Nav1.2, the N-terminal 116 residues, extracellular loop (residues 285-313), intracellular I-II linker (residues 442-739), II-III linker (residues 988-1190), and C-terminal sequences after Ser1786 were not modelled due to the lack of corresponding densities. 
Cross-references: PDB:6J8E
Protein: DP03178 (UniProt Q99250)
Region: residues 1786	to 2005
Annotation: disorder (Structural state)
Evidence: electron microscopy evidence used in manual assertion
Supporting statements:
For Nav1.2, the N-terminal 116 residues, extracellular loop (residues 285-313), intracellular I-II linker (residues 442-739), II-III linker (residues 988-1190), and C-terminal sequences after Ser1786 were not modelled due to the lack of corresponding densities. 
Cross-references: PDB:6J8E
Protein: DP03178 (UniProt Q99250)
Region: residues 442	to 739
Annotation: flexible linker (Disorder function)
Evidence: electron microscopy evidence used in manual assertion
Supporting statements:
For Nav1.2, the N-terminal 116 residues, extracellular loop (residues 285-313), intracellular I-II linker (residues 442-739), II-III linker (residues 988-1190), and C-terminal sequences after Ser1786 were not modelled due to the lack of corresponding densities.
Cross-references: PDB:6J8E
Protein: DP03178 (UniProt Q99250)
Region: residues 988	to 1190
Annotation: flexible linker (Disorder function)
Evidence: electron microscopy evidence used in manual assertion
Supporting statements:
For Nav1.2, the N-terminal 116 residues, extracellular loop (residues 285-313), intracellular I-II linker (residues 442-739), II-III linker (residues 988-1190), and C-terminal sequences after Ser1786 were not modelled due to the lack of corresponding densities.
Cross-references: PDB:6J8E
Protein: DP03178 (UniProt Q99250)
Region: residues 1777	to 1787
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model contains the NaV1.2 amino acids 1788-1929, FGF13U amino acids 11-158, and the CaM amino acids 7-149. The model was refined to Rwork/Rfree of 21.5/24.6 % (Table 1). 
The PDB evidence shows this region lacks electron density, indicating it is disordered.
Cross-references: PDB:4JPZ
Protein: DP03178 (UniProt Q99250)
Region: residues 1900	to 1905
Annotation: calmodulin binding (Molecular function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
Second, to test the proposed role of Arg1902 in the relayed interactions in NaV1.2 CTD/apoCaM, we measured the affinity of apoCaM for the wild type and Arg1902Cys mutant NaV1.2 CTDs by ITC. Consistent with our hypothesis, the Arg1902Cys mutation reduced affinity of apoCaM for the NaV1.2 CTD significantly (Table 3 and Supplementary Fig. 4C).
The ITC experiment with the CaM34 mutant showed a reduced affinity for the Arg1902Cys mutant compared to the wild CTD in the presence of Ca2+ (Table 3 and Supplementary Fig. 4E).
Protein: DP03179 (UniProt O95391)
Region: residues 1	to 61
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Importantly, the disordered portions of Slu7 (residues 1–61, 197–264, and 372–586) are highly enriched by positively charged amino acids: 62 Arg and Lys residues in total. 
The fine quality of the EM density map allows identification of two large segments of Slu7: residues 62–196 and 265–371 (Table S2).
Cross-references: PDB:5XJC
EMDB:EMD-6721
Protein: DP03179 (UniProt O95391)
Region: residues 197	to 264
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Importantly, the disordered portions of Slu7 (residues 1–61, 197–264, and 372–586) are highly enriched by positively charged amino acids: 62 Arg and Lys residues in total. 
The fine quality of the EM density map allows identification of two large segments of Slu7: residues 62–196 and 265–371 (Table S2).
Cross-references: PDB:5XJC
EMDB:EMD-6721
Protein: DP03179 (UniProt O95391)
Region: residues 372	to 586
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Importantly, the disordered portions of Slu7 (residues 1–61, 197–264, and 372–586) are highly enriched by positively charged amino acids: 62 Arg and Lys residues in total. 
The fine quality of the EM density map allows identification of two large segments of Slu7: residues 62–196 and 265–371 (Table S2).
Cross-references: PDB:5XJC
EMDB:EMD-6721
Protein: DP03180 (UniProt Q03692)
Region: residues 521	to 548
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Untagged collagen X NC1 domain produced in an in vitro expression system is stabilized significantly by the N-terminal segment. The most obvious interpretation of this observation is that a defined structure of the N-terminal segment contributes to NC1 trimer formation, yet this is not observed in our crystals.
Residues 549–680 have clear and continuous electron density; the N-terminal 28 residues and the His6 tag are not visible and are presumed to be disordered.
Cross-references: PDB:1GR3
Protein: DP03182 (UniProt Q17RS7)
Region: residues 243	to 307
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The EXO domain in GEN1 has a 78 amino acid insertion (residues 245–322), of which only helix α12b (residues 308–322) is ordered in the structure (Figure 1A, gray and Figure 2).
Cross-references: PDB:5T9J
Protein: DP03184 (UniProt P09919)
Region: residues 157	to 166
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Other sections were less precisely determined; in particular, residues -1 to 9, 65 to 70, 127 to 136, and 173 to 174 did not have convincing density.
This gave a noticeable improvement in the map quality; however, it was still not possible to locate the missing residues, which remain undefined even after refinement.
Cross-references: PDB:1RHG
Protein: DP03185 (UniProt O75223)
Region: residues 2	to 13
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The asymmetric unit of the structure contains two LOC79017 monomers and 141 water molecules. Several N‐ and C‐terminal residues (residues 1–13 and 183–188 for chain A; residues 1–14 and 184–188 for chain B) were not included in the model due to insufficient electron density. 
The starting Met is missing and the first residue  in the PDB is just a cloning artifact.
Cross-references: PDB:2Q53
PDB:2I5T
Protein: DP03185 (UniProt O75223)
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 structure comprises a dimer with continuous electron density observable for residues 14–182 in monomer A and residues 15–183 in monomer B as well as 34 water molecules. No electron density is apparent for the NH2-terminal 13 (monomer A) or 14 (monomer B) residues.
Cross-references: PDB:3CRY
PDB:2RBH
Protein: DP03186 (UniProt P28325)
Region: residues 21	to 31
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
No electron density was detected for the residues in the N-terminal segment before Ala10 (Fig. 1A). This region must thus be disordered in structure. 
Cross-references: PDB:1ROA
Protein: DP03186 (UniProt P28325)
Region: residues 21	to 30
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
No electron density was detected for the residues in the N-terminal segment before Ala10 (Fig. 1A). This region must thus be disordered in structure. 
Cross-references: PDB:1RN7
Protein: DP03187 (UniProt P43250)
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 final model contains residues 24–474 and 492–532 in chain A and residues 24–387, 391–473, and 492–535 in chain B (sup-plemental Fig. S1). Mass spectroscopic analysis of the protein used for crystallization suggests that the missing regions are disordered and not proteolyzed. The missing residues from positions 474/475 to 491 in each chain correspond to the so-called “nucleotide gate” region of the kinase domain (45), which was similarly disordered in structures of GRK2


Despite the statement in the publication that residues 1- 23 are disordered, reviewing of the PDB structure (https://ftp.wwpdb.org/pub/pdb/validation_reports/ac/2acx/2acx_full_validation.pdf.gz) shows three visible residues (14 - 16) in the aforementioned region.
Cross-references: PDB:2ACX
Protein: DP03187 (UniProt P43250)
Region: residues 475	to 491
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model contains residues 24–474 and 492–532 in chain A and residues 24–387, 391–473, and 492–535 in chain B (sup-plemental Fig. S1). Mass spectroscopic analysis of the protein used for crystallization suggests that the missing regions are disordered and not proteolyzed. The missing residues from positions 474/475 to 491 in each chain correspond to the so-called “nucleotide gate” region of the kinase domain (45), which was similarly disordered in structures of GRK2
Cross-references: PDB:2ACX
Protein: DP03187 (UniProt P43250)
Region: residues 536	to 576
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model contains residues 24–474 and 492–532 in chain A and residues 24–387, 391–473, and 492–535 in chain B (sup-plemental Fig. S1). Mass spectroscopic analysis of the protein used for crystallization suggests that the missing regions are disordered and not proteolyzed. The missing residues from positions 474/475 to 491 in each chain correspond to the so-called “nucleotide gate” region of the kinase domain (45), which was similarly disordered in structures of GRK2
Cross-references: PDB:2ACX
Protein: DP03190 (UniProt P49257)
Region: residues 176	to 185
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
 In the both structures, two loops comprised of residues 155–161 and 176–185 (termed Loops 1 and 2, respectively) of ERGIC-53, which were disordered in the Ca2+-free form.
Cross-references: PDB:3WNX
PDB:3WHU
Protein: DP03190 (UniProt P49257)
Region: residues 176	to 185
Annotation: metal ion binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
 In the both structures, two loops comprised of residues 155–161 and 176–185 (termed Loops 1 and 2, respectively) of ERGIC-53, which were disordered in the Ca2+-free form.
Protein: DP03190 (UniProt P49257)
Region: residues 176	to 185
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the both structures, two loops comprised of residues 155–161 and 176–185 (termed Loops 1 and 2, respectively) of ERGIC-53, which were disordered in the Ca2+-free form.
Cross-references: PDB:3WHT
Protein: DP03191 (UniProt P55145)
Region: residues 162	to 182
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Due to the poor quality of the MANF electron density maps in the C-terminus region, residues 99–137 were modelled as polyalanine, except for the disulphide bridge between C127 and C130, which was modelled based on density in a sulphur-anomalous map (Fig. 1B). Residues 138–158 are not visible at all.
The region 138-158 in the publication corresponds to region 162-182 because residues 1-24 are not in the crystal.
Cross-references: PDB:2W51
Protein: DP03192 (UniProt Q15013)
Region: residues 36	to 53
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 (residues 36-53) and the loop connecting helices αAB and αB (residues 97-118) in p31comet could not be located in the final electron density map and are likely disordered.
Cross-references: PDB:2QYF
Protein: DP03192 (UniProt Q15013)
Region: residues 97	to 118
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 (residues 36-53) and the loop connecting helices αAB and αB (residues 97-118) in p31comet could not be located in the final electron density map and are likely disordered.
The construct differs from the canonical sequence as Met108 is a modified residue, i.e. a selenomethionine.
Cross-references: PDB:2QYF
Protein: DP03193 (UniProt P16869)
Region: residues 37	to 57
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
No direct statement on Intrinsic Disorder is given either in the paper or the supplementary information. However, (i) there exists such information within the PDB file (REMARK 465 MISSING RESIDUES) and (ii) the authors clearly state within the manuscript that the N-terminal signal peptide (AAs 1-36) was removed for protein production.
Cross-references: PDB:6E4V
Protein: DP03195 (UniProt Q9HAV4)
Region: residues 474	to 490
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
We modeled 1082 of 1204 residues of Exp-5. Several loop regions in the 20 HEAT repeats and 55 residues at the C terminus could not be modeled (details in fig. S1), and 13 residues at the C terminus were modeled as a polyalanine a helix.
The N-terminal residue 1, residues 474-490 in the loop of HEAT12, residues 705-706 in the loop of HEAT14, residues 938-951 in the loop of HEAT17 and residues 980-1069 in the loop between HEAT17 and HEAT18 are disordered in the crystal. Out of 68 C-terminal residues, 55 residues were not modeled because of disordered structure, and 13 residues were built as a poly-alanine α-helix because of high temperature factor.
This feature corresponds to the IDR in the loop of HEAT10 as shown in Supplementary Fig. S1. The respective author statement, taken from the legend of Fig. S1, erroneously refers to the loop for HEAT12. See Supplementary Fig. S1 for more details.
Cross-references: PDB:3A6P
Protein: DP03195 (UniProt Q9HAV4)
Region: residues 938	to 951
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
We modeled 1082 of 1204 residues of Exp-5. Several loop regions in the 20 HEAT repeats and 55 residues at the C terminus could not be modeled (details in fig. S1), and 13 residues at the C terminus were modeled as a polyalanine a helix.
The N-terminal residue 1, residues 474-490 in the loop of HEAT12, residues 705-706 in the loop of HEAT14, residues 938-951 in the loop of HEAT17 and residues 980-1069 in the loop between HEAT17 and HEAT18 are disordered in the crystal. Out of 68 C-terminal residues, 55 residues were not modeled because of disordered structure, and 13 residues were built as a poly-alanine α-helix because of high temperature factor.
This feature corresponds to the IDR in the loop of HEAT17.
Cross-references: PDB:3A6P