LiteFold/DisProt huggingface dataset:
Protein: DP03019 (UniProt P30996)
Region: residues 249	to 260
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The loop region Asp205-Thr214 is disordered and not modeled in both structures. Loop Glu249-Ile262 disordered and hence not modeled in form I is ordered in the form II crystal. The C-terminal residues (Val422- Lys439) are not modeled due to poor electron density in both structures. The absence of the C-terminal residues and the disordered region (Glu249-Ile262) is not due to autolysis as shown by SDS-PAGE analysis on crystals of both forms (data not shown) (24, 25).”
Cross-references: PDB:2A97
Protein: DP03019 (UniProt P30996)
Region: residues 416	to 439
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The loop region Asp205-Thr214 is disordered and not modeled in both structures. Loop Glu249-Ile262 disordered and hence not modeled in form I is ordered in the form II crystal. The C-terminal residues (Val422- Lys439) are not modeled due to poor electron density in both structures. The absence of the C-terminal residues and the disordered region (Glu249-Ile262) is not due to autolysis as shown by SDS-PAGE analysis on crystals of both forms (data not shown) (24, 25).”
Cross-references: PDB:2A97
PDB:2A8A
Protein: DP03020 (UniProt O06522)
Region: residues 18	to 56
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-terminal 38 residues (18–56) of the crystallized construct of CdtA are not visible in the electron density, nor are residues 183–185 of CdtB (internal loop). 

It is probable, therefore, that residues 18–67 are normally disordered in the complex, but a fortuitous crystal-packing arrangement allowed for the region between 56 and 67 to become ordered
Cross-references: PDB:1SR4
Protein: DP03021 (UniProt F2WK69)
Region: residues 88	to 164
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The structural model contains CdiA-CTo11 EC869 residues Val85 – Lys297 (numbered from Val1 of the VENN motif) and Ala2 – Arg164 of CdiIo11 EC869
In contrast, the CdiA-CT N-terminal regions are not fully resolved in the structures and their functional significance remains unclear. The N-terminal regions are exceptionally labile to proteolysis, suggesting these domains are flexible and perhaps partially disordered. Intrinsically flexible domains are critical for colicin toxin import (23, 24), so perhaps the N-terminal region mediates CdiA-CT transport across the target cell envelope
Residue V85 mentioned by the authors, refers to residue V165 of the UNIPROT sequence and residue K297 corresponds to residue K377 of the UNIPROT sequence
Cross-references: PDB:4G6U
Protein: DP03022 (UniProt I1WVY3)
Region: residues 2948	to 2987
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The structural model contains CdiA-CTII Bp1026b residues Gly163 – Pro294 and residues Ala2 – Arg101 of CdiIII Bp1026b
The CdiA-CTo11 EC869/CdiIo11 EC869 complex was stable; however, the N-terminus of the CdiA-CTII Bp1026b showed significant degradation after purification, suggesting that this region is sensitive to proteolysis
In contrast, the CdiA-CT N-terminal regions are not fully resolved in the structures and their functional significance remains unclear. The N-terminal regions are exceptionally labile to proteolysis, suggesting these domains are flexible and perhaps partially disordered. Intrinsically flexible domains are critical for colicin toxin import (23, 24), so perhaps the N-terminal region mediates CdiA-CT transport across the target cell envelope.
Residue G163 mentioned by the authors, refers to residue G2988 of the UNIPROT sequence and P294 refers to residue 3119 of the UNIPROT sequence
Cross-references: PDB:4G6V
Protein: DP03023 (UniProt P43528)
Region: residues 251	to 263
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
However, the A2 linkers share only 38% sequence identity between LT-IIa and LT-IIb and have only 21% sequence
identity with LT-I [10,11].”

In addition, the C-terminal residues 231–243 of the A2 chain could not be traced. However, substantial yet uninterpretable electron density in the pore persists in Fo–Fc maps contoured at the 2s level, indicating a partially disordered conformation for these terminal residues
The residues referred to by the authors as 231-243 correspond to UNIPROT entry residues 251-263
Cross-references: PDB:1TII
Protein: DP03023 (UniProt P43528)
Region: residues 251	to 263
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The lower part of the pore holds the remaining 13 C-terminal residues, for which some electron density is present. Since the last interpretable residue (Asn230) is already two-thirds of the way down the 30 Å long pore (Fig. 8), it seems likely that not all 13 remaining residues will fit inside the lower part of the pore. The four C-terminal residues lysine, aspartate, glutamate, leucine (KDEL) in the A2 fragment of LT-IIb, being an endoplasmic reticulum (ER) retention signal [48], will thus most likely extend outside the pore, similar to the arginine, aspartate, glutamate, leucine (RDEL) terminus in LT-I [3,4].

In LT-IIb, residue 230 is not part of the helix and residues 231–243 could not be fit in the uninterpretable electron density present in the lower half of the pore. The interactions between A2 and the B pentamer in the upper part of the pore are entirely hydrophobic in nature by means of Phe220, Thr221, Leu222, Met223, Thr224, Leu225, Leu226, and Ile228 of A2 interacting with Met69, Ala70, Leu73 and the Cb of Ser74 of each of the B subunits. In fact, upon A2–B5 association, a surface of 1127 Å2 is buried, of which 869 Å2 is hydrophobic.

The residues referred to by the authors as 231-243 correspond to UNIPROT entry residues 251-263
Cross-references: PDB:1TII
Protein: DP03023 (UniProt P43528)
Region: residues 251	to 263
Annotation: molecular adaptor activity (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The lower part of the pore holds the remaining 13 C-terminal residues, for which some electron density is present. Since the last interpretable residue (Asn230) is already two-thirds of the way down the 30 Å long pore (Fig. 8), it seems likely that not all 13 remaining residues will fit inside the lower part of the pore. The four C-terminal residues lysine, aspartate, glutamate, leucine (KDEL) in the A2 fragment of LT-IIb, being an endoplasmic reticulum (ER) retention signal [48], will thus most likely extend outside the pore, similar to the arginine, aspartate, glutamate, leucine (RDEL) terminus in LT-I [3,4].

In LT-IIb, residue 230 is not part of the helix and residues 231–243 could not be fit in the uninterpretable electron density present in the lower half of the pore. The interactions between A2 and the B pentamer in the upper part of the pore are entirely hydrophobic in nature by means of Phe220, Thr221, Leu222, Met223, Thr224, Leu225, Leu226, and Ile228 of A2 interacting with Met69, Ala70, Leu73 and the Cb of Ser74 of each of the B subunits. In fact, upon A2–B5 association, a surface of 1127 Å2 is buried, of which 869 Å2 is hydrophobic.

The residues referred to by the authors as 231-243 correspond to UNIPROT entry residues 251-263
Cross-references: PDB:1TII
Protein: DP03023 (UniProt P43528)
Region: residues 258	to 263
Annotation: localization (Biological process)
Evidence: author inference used in manual assertion
Supporting statements:
The four C-terminal residues lysine, aspartate, glutamate, leucine (KDEL) in the A2 fragment of LT-IIb, being an endoplasmic reticulum (ER) retention signal [48], will thus most likely extend outside the pore, similar to the arginine, aspartate, glutamate, leucine (RDEL) terminus in LT-I [3,4].
The involvement of the ER retention signal in LT intoxication has been postulated. However, recent studies have reached different conclusions concerning the role of RDEL/KDEL-dependent retrograde transport through the Golgi-ER during intoxication by CT and LT-I [49,50]
Cross-references: PDB:1TII
Protein: DP03024 (UniProt Q7B8V4)
Region: residues 199	to 210
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Our structure further demonstrates the remarkable plasticity of the substrate binding cleft of the BoNT/
A LC protease and provides a paradigm for iterative structure-based design and development of BoNT/A LC inhibitors

residues 199-210 are disordered in the structure
Cross-references: PDB:3NF3
Protein: DP03024 (UniProt Q7B8V4)
Region: residues 245	to 255
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Our structure further demonstrates the remarkable plasticity of the substrate binding cleft of the BoNT/
A LC protease and provides a paradigm for iterative structure-based design and development of BoNT/A LC inhibitors

Electron density for the 250 loop of the BoNT/A LC is only observed for structures of the LC complexed with PLMs containing either no side chain (i.e. a Gly component) or an Ala in the P29 position (Figure 7C). In contrast, no electron density is observed for various residues within this loop for either the unbound form of the BoNT/A LC, or when bound to arginine hydroxamate (ArgHX) (residues 245–256), I1 (residues 250–253), or JTH-NB72-39 (residues 247–255) (Figure 7C). In all BoNT/A LC:inhibitor complexes described
Cross-references: PDB:3NF3
Protein: DP03026 (UniProt A0A384E149)
Region: residues 414	to 439
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 1–413 were clearly defined, however no electron density was observed for the N-terminal tag and the C-terminal end (414–439), all in solvent-accessible areas
Cross-references: PDB:6F47
PDB:6F4E
Protein: DP03027 (UniProt Q81AN8)
Region: residues 319	to 329
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In the WT domain, dynamic flexibility occurs at the N-terminus and the first α-helix that connects the HlyIIC domain to the HlyII-core structure. In the destabilizing P405M mutant, increased flexibility is evident throughout the first subdomain

As shown in Fig. 4A, most residues in the regular secondary structure HlyIIC have S 2 order parameters in the rigid limit. Low S2 order parameters indicative of dynamic flexibility occur for the N-terminal segment that connects HlyIIC to the rest of the HlyII protein, the N-terminal α-helix (αA), and the loops between secondary structure units - in particular the loop between helix αB and strand β5 that includes the site of the P405M mutation. The dynamic nature of the N-terminal linker segment corresponding to the first 11 amino acids of HlyIIC appears to be conserved in the full-length HlyII toxin, in as much as HlyIIC can be proteolytically cleaved from HlyII
The non-zero R2ex terms are due to conformational exchange on the µs-ms timescale. The majority of residues that experience R2ex contributions are in the two helices αA and αB
Figure 1 legend: The first 11 residues at the disordered N-terminus are not shown.
The region is a linker between two ordered domains, and the BMRB code attached is for the P405M mutant, for which the 3D structure was calculated and the relaxation data was measured.
Cross-references: PDB:2N67
BMRB:19463
Protein: DP03027 (UniProt Q81AN8)
Region: residues 319	to 329
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy-based hydrogen-deuterium exchange evidence used in manual assertion
Supporting statements:
In the WT domain, dynamic flexibility occurs at the N-terminus and the first α-helix that connects the HlyIIC domain to the HlyII-core structure. In the destabilizing P405M mutant, increased flexibility is evident throughout the first subdomain

Backbone amide proton protection factors in WT-HlyIIC are uniformly large for residues in regular secondary structure. The exception is helix αA, where only a single residue shows weak protection (Fig. 5B,D). In the P405M mutant (Fig. 5C), the largest protection factors are reduced about 2.5-fold compared to WT, consistent with the lower stability of the mutant to unfolding (Fig. 3B). A much more dramatic change is seen when the structure distribution of protection factors in the P405M mutant is considered. The amide protons from subdomain 2 in the second half of the molecule are protected but only two amide protons from subdomain 1 show measurable protection, at the beginning of strand β2 (Fig. 5C,E)
Cross-references: PDB:2N67
Protein: DP03027 (UniProt Q81AN8)
Region: residues 319	to 329
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In the WT domain, dynamic flexibility occurs at the N-terminus and the first α-helix that connects the HlyIIC domain to the HlyII-core structure. In the destabilizing P405M mutant, increased flexibility is evident throughout the first subdomain

Backbone amide proton protection factors in WT-HlyIIC are uniformly large for residues in regular secondary structure. The exception is helix αA, where only a single residue shows weak protection (Fig. 5B,D). In the P405M mutant (Fig. 5C), the largest protection factors are reduced about 2.5-fold compared to WT, consistent with the lower stability of the mutant to unfolding (Fig. 3B). A much more dramatic change is seen when the structure distribution of protection factors in the P405M mutant is considered. The amide protons from subdomain 2 in the second half of the molecule are protected but only two amide protons from subdomain 1 show measurable protection, at the beginning of strand β2 (Fig. 5C,E)
The dynamic nature of the N-terminal linker segment corresponding to the first 11 amino acids of HlyIIC appears to be conserved in the full-length HlyII toxin, in as much as HlyIIC can be proteolytically cleaved from HlyII
In the monomer model (Fig. 6A), the HlyIIC domain extends from the toxin core at an edge of the β-sandwich structure opposite that of the stem loop, so that an interaction between the two segments is highly unlikely. Fig. 6B and C show the homology model of the heptameric membrane-spanning pore complex. Even with a fully extended linker, the domain appears to be too far away to interact with the pore component of the structure (Fig. 6B and C), in agreement with experimental results that indicate HlyIIC does not obstruct the toxin pore in voltage gating experiments
The linker segment between the N-terminus of HlyIIC domain and the C-terminus of the HlyII core is highly flexible and can be proteolytically cleaved
Cross-references: PDB:2N67
Protein: DP03027 (UniProt Q81AN8)
Region: residues 319	to 329
Annotation: flexible linker (Disorder function)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Limited proteolysis of the oligomers formed by HlyII and HlyII(ΔCT) on red cell membranes showed that the C‐terminal extension is sensitive to digestion, while HlyII(ΔCT) is protease resistant and migrates with an electrophoretic mobility similar to that of digested HlyII

multiple proteolytic fragments at low protease concentrations (5 μg mL−1; Fig. 3, lane 2). In contrast, the oligomeric form of HlyII(ΔCT), like the αHL heptamer, was protease resistant. At the highest concentration of proteinase K (500 μg mL−1), a protease‐resistant, SDS‐stable form of oligomeric HlyII was formed, which migrated in SDS gels with a similar mobility to oligomers formed from the genetically truncated HlyII(ΔCT) (Fig. 3). These results suggest that the C‐terminal extension either has a structure with pronounced sensitivity to proteolytic cleavage, or that the extension is connected to the rest of the protein through a readily accessible linker. The former is favored because the C terminus (TL, see below) expressed as a separate domain is protease sensitive (data not shown)
In the monomer model (Fig. 6A), the HlyIIC domain extends from the toxin core at an edge of the β-sandwich structure opposite that of the stem loop, so that an interaction between the two segments is highly unlikely. Fig. 6B and C show the homology model of the heptameric membrane-spanning pore complex. Even with a fully extended linker, the domain appears to be too far away to interact with the pore component of the structure (Fig. 6B and C), in agreement with experimental results that indicate HlyIIC does not obstruct the toxin pore in voltage gating experiments
The N terminal domain is defined between residues 1-288 in this paper, which corresponds to residues 31 to 318 of the Uniprot entry, and the C terminal domain is defined in this paper as residues 289-382, which corresponds to residues 319-412 of the Uniprot entry. This is consistent with the presence of the signal peptide in the Uniprot entry and the fact that this is a secreted protein.
Protein: DP03028 (UniProt A0A0H3GD84)
Region: residues 25	to 38
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
While the PEST-like sequence (aa 39–51) is well resolved (Fig. 2), the preceding residues 25–38 are, due to their flexibility, not visible in the structure.
Protein: DP03029 (UniProt Q9ZKK2)
Region: residues 1	to 11
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
We have determined the crystal structure of JHP933 at 2.17 A ̊resolution. The refined model contains 452 residues from two monomers of the recombinant JHP933 and 257 water molecules in the crystallographic asymmetric unit. It encompasses the residues 12–232 ofJHP933 and four (or six) residues of the C-terminal tag in chain A (or B). 
Cross-references: PDB:4OK0
Protein: DP03032 (UniProt P76063)
Region: residues 80	to 98
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We show that, contrary to expectation, YdaS behaves as a monomer and contains an intrinsically disordered region at its C-terminus. This makes it the representative of a fourth yet uncharacterized class of HigA proteins.
Predicted from the backbone chemical shifts using the chemical  shift  index  (CSI)  function  and  the  DANGLE  module (Cheung et al. 2010) in CCPNMR, the secondary structure of YdaS consists of five short α-helices, followed by a tail that contains several isolated residues with a high propensity for β-strand. There is, however, only a single such stretch (residues 80–90) that contains three residues, which indicates that likely no real β-sheet is formed and that the C-terminal tail lacks regular secondary structure (Fig. 3).
Cross-references: BMRB:27917
Protein: DP03034 (UniProt Q48245)
Region: residues 333	to 367
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
It is likely that the two missing regions, residues 1–26 in p33 domain and 300–334 between p33 and p55 domains, in our current map are highly flexible.
Authors mention region 300-334. Although these boundaries are true for the protein chain without signal peptide, they correspond to region 333-367 in the UniProt sequence. The 1-26 short hydrophobic region was told to be inserted into the membrane in the native protein, so it cannot be considered as disordered, this is why it was not annotated separately.
Cross-references: PDB:6NYJ
PDB:6NYF
PDB:6NYN
PDB:6NYM
PDB:6NYL
PDB:6NYG
Protein: DP03034 (UniProt Q48245)
Region: residues 339	to 350
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Partial proteolytic digestion of the mature secreted 88-kDa VacA toxin yields two fragments that are ∼33 and 55 kDa in mass (p33 and p55, respectively) (see Fig. 1A). This proteolytic cleavage occurs primarily between amino acids 311 and 312 of the mature secreted toxin from H. pylori strain 60190 (and possibly several adjacent sites) (27), which are predicted to comprise a hydrophilic surface-exposed loop of VacA.
The authors do not define the precise length of the digested region but mention that several neighboring residues might also be affected, therefore I have added 5 residues on each side of the two residues named as the primary cleavage site. Authors mention residues 311-312, but those correspond to residues 344-345 in the UniProt sequence due to the presence of a 33 residues long signal peptide in the latter.
Protein: DP03034 (UniProt Q48245)
Region: residues 339	to 350
Annotation: flexible linker (Disorder function)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Partial proteolytic digestion of the mature secreted 88-kDa VacA toxin yields two fragments that are ∼33 and 55 kDa in mass (p33 and p55, respectively) (see Fig. 1A). This proteolytic cleavage occurs primarily between amino acids 311 and 312 of the mature secreted toxin from H. pylori strain 60190 (and possibly several adjacent sites) (27), which are predicted to comprise a hydrophilic surface-exposed loop of VacA. It has been suggested that the p33 and p55 fragments represent two domains or subunits of VacA.
The authors do not define the precise length of the digested region but mention that several neighboring residues might also be affected, therefore I have added 5 residues on each side of the two residues named as the primary cleavage site. Authors mention residues 311-312, but those correspond to residues 344-345 in the UniProt sequence due to the presence of a 33 residues long signal peptide in the latter.
Protein: DP03035 (UniProt P35269)
Region: residues 55	to 92
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The cryo-EM structure of the transcription pre-initiation complex (PIC) shows this region of the General transcription factor IIF subunit 1 lacks electron density, indicating it is disordered.
Cross-references: PDB:5IYB
PDB:5IY8
Protein: DP03037 (UniProt Q96GX5)
Region: residues 855	to 879
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
However, the active-site tether (AST) region at the extreme C-terminus of hGWL-KinDom is not visible (aa 855-879) despite being encoded in the expression construct.
Cross-references: PDB:5LOH
Protein: DP03039 (UniProt Q00653)
Region: residues 702	to 725
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
A long acidic insert (residues 702–725) between AR6 and AR7 is disordered.
Cross-references: PDB:4OT9