LiteFold/DisProt huggingface dataset:
Protein: DP04028 (UniProt Q9CA59)
Region: residues 225	to 255
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Although our previous study showed that
NRP1 CTAD (amino acids 225 to 255) contributes to H2A-H2B
binding and is important for the function of NRP1 in planta (18),
the CTAD domain was disordered in the NRP1-H2A-H2B
complex.
The CTAD domain is invisible in the electron density map.
Cross-references: PDB:7C7X
Protein: DP04028 (UniProt Q9CA59)
Region: residues 226	to 232
Annotation: histone binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Finally, we solved three crystal
structures of C-terminal acidic domains (CTADs) of NRP1 and
human NAP1 in complex with H2A-H2B, revealing a conserved
histone binding mode among NAP1 family proteins.
To reveal how NRP1 CTAD interacts with H2A-H2B, we solved the structure of H2A-H2B in complex with CTAD peptide D226-F232 (SI Appendix, Table S2). All seven residues (D226 to F232) of CTAD are well ordered in the cocrystal structure and engage H2A L2 and H2B L1 (Fig. 4A), and electronegative residues D228, E229, E230, and D231 within NRP1 CTAD are cocooned by the positively charged groove of H2A-H2B (SI Appendix, Fig. S6A).
Cross-references: PDB:7BP6
Protein: DP04028 (UniProt Q9CA59)
Region: residues 165	to 184
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The structure deposited in PDB shows this region lacks electron density, indicating it is disordered.
Cross-references: PDB:7C7X
Protein: DP04028 (UniProt Q9CA59)
Region: residues 194	to 203
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The structure deposited in PDB shows this region lacks electron density, indicating it is disordered.
Cross-references: PDB:7C7X
Protein: DP04029 (UniProt Q94A79)
Region: residues 1	to 42
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
N-terminal region aa. 1–42 and C-terminal region aa. 410–420 were not visible in all DMS3 monomers of our structures, probably due to flexibility.
Cross-references: PDB:6OIT
PDB:6OIS
Protein: DP04029 (UniProt Q94A79)
Region: residues 410	to 420
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
N-terminal region aa. 1–42 and C-terminal region aa. 410–420 were not visible in all DMS3 monomers of our structures, probably due to flexibility.
Cross-references: PDB:6OIT
PDB:6OIS
Protein: DP04030 (UniProt P41743)
Region: residues 233	to 248
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with high relative B-factor values used in manual assertion
Supporting statements:
Amino acid stretches with
high B-values and therefore poorly defined electron
density are: residues 224–239 from the N terminus,
446–454 from the PKCi extended loop, 533–551 from
the turn motif and 580–587 at the very C terminus.
The numbering of the amino acids in the structure is shifted compared to the reference sequence in Uniprot.
Cross-references: PDB:1ZRZ
Protein: DP04030 (UniProt P41743)
Region: residues 542	to 560
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with high relative B-factor values used in manual assertion
Supporting statements:
Amino acid stretches with
high B-values and therefore poorly defined electron
density are: residues 224–239 from the N terminus,
446–454 from the PKCi extended loop, 533–551 from
the turn motif and 580–587 at the very C terminus.
The numbering of the amino acids in the structure is shifted compared to the reference sequence in Uniprot.
Cross-references: PDB:1ZRZ
Protein: DP04032 (UniProt Q6ZT98)
Region: residues 236	to 268
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Ribbon representation of the TTLL7 core bound to ADP. Nucleotide shown as a stick model. Spheres represent disordered polypeptide chain regions. c-MTBD residues, orange spheres.
Cross-references: PDB:4YLR
PDB:4YLS
Protein: DP04032 (UniProt Q6ZT98)
Region: residues 383	to 450
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Ribbon representation of the TTLL7 core bound to ADP. Nucleotide shown as a stick model. Spheres represent disordered polypeptide chain regions. c-MTBD residues, orange spheres.
Cross-references: PDB:4YLR
PDB:4YLS
Protein: DP04032 (UniProt Q6ZT98)
Region: residues 485	to 518
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Ribbon representation of the TTLL7 core bound to ADP. Nucleotide shown as a stick model. Spheres represent disordered polypeptide chain regions. c-MTBD residues, orange spheres.
Cross-references: PDB:4YLR
PDB:4YLS
Protein: DP04033 (UniProt O15431)
Region: residues 1	to 52
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The measured spectra were in good agreement with the theoretical spectra predicted for the conformational ensembles obtained with HREX, validating the identified structures. In the absence of Cu(I) ions, the experimental CD spectrum exhibited a strong negative band at 200 nm, in agreement with that calculated for the Nterm in the unfolded state.
Protein: DP04033 (UniProt O15431)
Region: residues 1	to 52
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Conversely, measuring in the presence of sodium dodecyl sulfate (SDS) micelles, previously reported to affect Nterm conformation (19), resulted in an additional negative peak at 220 nm, corresponding to the CD spectrum predicted for the alpha state. Taken together, this suggests the conformation of the Nterm is modulated by the presence of Cu(I) ions and lipid molecules. While Cu(I) binding promotes the transition of the Nterm from the unfolded to the beta conformation, the interaction with lipid molecules leads to the formation of α-helical fragments as seen in the alpha state.
Protein: DP04033 (UniProt O15431)
Region: residues 1	to 52
Annotation: flexible N-terminal tail (Disorder function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The measured spectra were in good agreement with the theoretical spectra predicted for the conformational ensembles obtained with HREX, validating the identified structures. In the absence of Cu(I) ions, the experimental CD spectrum exhibited a strong negative band at 200 nm, in agreement with that calculated for the Nterm in the unfolded state.
Protein: DP04033 (UniProt O15431)
Region: residues 1	to 52
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The addition of Cu(I) ions reduced the depth of the minimum, so that the experimental CD spectrum matched that calculated for the beta state.
Protein: DP04033 (UniProt O15431)
Region: residues 1	to 52
Annotation: copper ion binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
While Cu(I) binding promotes the transition of the Nterm from the unfolded to the beta conformation, the interaction with lipid molecules leads to the formation of α-helical fragments as seen in the alpha state.
Protein: DP04035 (UniProt Q8RN04)
Region: residues 70	to 82
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
There
is very weak electron density for most of the region corresponding
to the B'-helix in one of the AS crystal forms, whereas in the
PEG crystal form the residues between Arg65 and Glu83 are
missing.
Table 1 also indicates missing residues.
Cross-references: PDB:1LFK
Protein: DP04036 (UniProt Q6FML9)
Region: residues 227	to 236
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Dotted lines
indicate the loop regions, which were not observed in the electron density
maps.
Cross-references: PDB:4XM5
Protein: DP04036 (UniProt Q6FML9)
Region: residues 92	to 105
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Dotted lines
indicate the loop regions, which were not observed in the electron density
maps.
Cross-references: PDB:4XLG
Protein: DP04036 (UniProt Q6FML9)
Region: residues 301	to 312
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Dotted lines
indicate the loop regions, which were not observed in the electron density
maps.
Cross-references: PDB:4XLG
Protein: DP04037 (UniProt E9ADE1)
Region: residues 101	to 121
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
LeishIF4E-1 has
a 17 residue insertion in Loop 1 (L1, 104–120) and a 7
residue insertion in Loop 2 (L2, 151–157) (Supplementary
Figure S1A), which are disordered in our crystal structure
(residues 101–121, residues 149–155).
Disordered segments in loops (L1 and L2) from LeishIF4E-1 are shown in dashed
lines.
Cross-references: PDB:5WB5
Protein: DP04038 (UniProt Q06069)
Region: residues 68	to 80
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 1–6) and the loop
region (residues 68–80) between α3 and α4 were disordered
because the electron density was too weak to be detected
for building a structural model in those regions. 
Cross-references: PDB:5XNT
Protein: DP04039 (UniProt Q4QF76)
Region: residues 170	to 199
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The so-called resolving cysteine Cys173, the second residue essential for activity,
is not visible since it is located in the C-terminal portion of the
polypeptide that is disordered in all the monomers.
Cross-references: PDB:3TUE
Protein: DP04039 (UniProt Q4QF76)
Region: residues 170	to 199
Annotation: order (Structural state)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
We previously reported a lower resolution (3.00 Å) structure of the same protein in the reduced form and LU conformation (LmTXNPs-LU; PDB ID: 3TUE)11.
The significant gain in resolution may be ascribed to the reduced flexibility of the 169–199 region, which is fully visible in the FF conformation structure here presented and absent in the previously reported LU conformation structure.
Since the oxidized LmTXNPx state is generally associated with the LU conformation, structure comparison between the here reported LmTXNPx-FF and the previously solved LmTXNPx-LU structures provided us with the opportunity to infer the mechanism underlying the transition from FF to LU conformation that occurs upon protein oxidation.
Protein oxidation promotes a transition to a locally unfolded (LU) conformation, where: i) the α-helical turn containing Cp unwinds and rotates toward the solvent; and ii) the C-terminal tail unfolds and becomes disordered.
Cross-references: PDB:4K1F
Protein: DP04039 (UniProt Q4QF76)
Region: residues 170	to 199
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
We previously reported a lower resolution (3.00 Å) structure of the same protein in the reduced form and LU conformation (LmTXNPs-LU; PDB ID: 3TUE)11.
The significant gain in resolution may be ascribed to the reduced flexibility of the 169–199 region, which is fully visible in the FF conformation structure here presented and absent in the previously reported LU conformation structure.
Since the oxidized LmTXNPx state is generally associated with the LU conformation, structure comparison between the here reported LmTXNPx-FF and the previously solved LmTXNPx-LU structures provided us with the opportunity to infer the mechanism underlying the transition from FF to LU conformation that occurs upon protein oxidation.
Protein oxidation promotes a transition to a locally unfolded (LU) conformation, where: i) the α-helical turn containing Cp unwinds and rotates toward the solvent; and ii) the C-terminal tail unfolds and becomes disordered.
Cross-references: PDB:4K1F
PDB:3TUE
Protein: DP04040 (UniProt Q9TZX2)
Region: residues 179	to 188
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The 18 residues of C-terminal form a flexible tail containing an essential conserved Cys173. Subunits B, C, G, H and I were modelled up to or beyond residue Cys173 allowing the position of this important residue to be determined.
A b-hairpin (b6 and
b7) completes the b-sheet and leads to helix a4,
then finally a disordered C-terminal loop.
As it is also mention in the main text: "Subunits B, C,
G, H and I were modelled up to or beyond residue
Cys173 allowing the position of this important residue
to be determined." disordered region in the distinct chains starts differently.
Cross-references: PDB:1E2Y
Protein: DP04041 (UniProt O77103)
Region: residues 218	to 235
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In such structure, the region beyond residue 217 was found to be
disordered, yet several attempts to model ordered protein
atoms throughout it were unsuccessful.
Cross-references: PDB:1MZV
Protein: DP04042 (UniProt O00834)
Region: residues 17	to 27
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 17–28 and 262 likely
exhibit a degree of flexibility and therefore could not be
observed in the crystal structure.
In this structure, the last missing amino acid is His27 instead of Ser28 like in the two other structures.
Cross-references: PDB:2JH1
Protein: DP04044 (UniProt P50489)
Region: residues 351	to 387
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Similarly,
exposing a functional receptor-binding groove on AMA1 requires
displacement of the extended non-polymorphic DII loop, which
adopts a disordered state (not modeled between Lys351 to
Ala387); this region is stabilized by DI in apo PfAMA1 (Fig. 2B).
Cross-references: PDB:3SRI
Protein: DP04044 (UniProt P50489)
Region: residues 261	to 272
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This region is not mentioned in the publication, but the structure deposited in PDB indicates this region is unstructured.
Cross-references: PDB:3SRI
Protein: DP04045 (UniProt Q7KQK5)
Region: residues 351	to 387
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Similarly,
exposing a functional receptor-binding groove on AMA1 requires
displacement of the extended non-polymorphic DII loop, which
adopts a disordered state (not modeled between Lys351 to
Ala387); this region is stabilized by DI in apo PfAMA1 (Fig. 2B).
Cross-references: PDB:3ZWZ
Protein: DP04046 (UniProt P62368)
Region: residues 82	to 97
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Electron density is
absent or poorly defined for the loop linking α2 to α3 in
many of the IspF structures. 
Cross-references: PDB:4C82
PDB:4C81
Protein: DP04048 (UniProt Q9U1D9)
Region: residues 1	to 18
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
There
was no reliable electron density for the first 18 residues and
the model comprises residues Glu19–Ser125.
Cross-references: PDB:4CQI
Protein: DP04049 (UniProt Q86MV5)
Region: residues 20	to 29
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In all, 10 residues from the
N-terminus as well as 14 residues from the C-terminus were
disordered and not incorporated into the structures.
Cross-references: PDB:2B51
PDB:2B56
PDB:2B4V
Protein: DP04049 (UniProt Q86MV5)
Region: residues 474	to 487
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In all, 10 residues from the
N-terminus as well as 14 residues from the C-terminus were
disordered and not incorporated into the structures.
Cross-references: PDB:2B56
PDB:2B51
Protein: DP04050 (UniProt Q257B3)
Region: residues 314	to 345
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The 32-residue C-terminal extension of tTFIIBC
(residues 314–345) is not visible in the crystal, suggesting that it is
unstructured.
Cross-references: PDB:3H4C
Protein: DP04050 (UniProt Q257B3)
Region: residues 262	to 274
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The linker (residues 162–174), which
connects H3'A to H4', is not visible in the electron density,
suggesting that it is unstructured.
The numbering is incorrect in the text, but correct in Fig.2C.
Cross-references: PDB:3H4C
Protein: DP04050 (UniProt Q257B3)
Region: residues 262	to 274
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The linker (residues 162–174), which connects H3'A to H4', is not visible in the electron density, suggesting that it is unstructured.
The numbering is incorrect in the text, but correct in Fig.2C.
Cross-references: PDB:3H4C
Protein: DP04051 (UniProt Q8IJ45)
Region: residues 375	to 389
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The loop
between helices 6 and 7 (residues 374 –388) was disordered (Fig. 6), as has been observed for other DBL structures (e.g.
PfEMP1 VAR2CSA DBL 6ε,, PDB code 2WAU) (38).
Cross-references: PDB:3VUU
PDB:3VUV
Protein: DP04051 (UniProt Q8IJ45)
Region: residues 375	to 389
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The loop between helices 6 and 7 (residues 374 –388) was disordered (Fig. 6), as has been observed for other DBL structures (e.g. PfEMP1 VAR2CSA DBL 6ε,, PDB code 2WAU) (38).
Cross-references: PDB:3VUU
PDB:3VUV
Protein: DP04052 (UniProt Q8I639)
Region: residues 2333	to 2349
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Subdomain 1 of DBL6ε consists of residues 2333–2390 with residues 2333–2348 disordered in the crystal.
Cross-references: PDB:2WAU
Protein: DP04054 (UniProt Q57WT9)
Region: residues 210	to 246
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final electron density for the
TbASNA model is well defined except for loop 1 (residues
51–57) and loop 2 (residues 210–250; Figs. 7–9).
The significance of this insertion at this location in the
structure of TbASNA is unclear because in the crystal structure
of apo-TbASNA this loop is completely disordered.
Cross-references: PDB:4LNS
Protein: DP04054 (UniProt Q57WT9)
Region: residues 210	to 246
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final electron density for the TbASNA model is well defined except for loop 1 (residues 51–57) and loop 2 (residues 210–250; Figs. 7–9).
The significance of this insertion at this location in the structure of TbASNA is unclear because in the crystal structure of apo-TbASNA this loop is completely disordered.
Cross-references: PDB:4LNS
Protein: DP04055 (UniProt Q2WF71)
Region: residues 233	to 242
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Ten
residues between the seventh and eighth repeats were disordered.
Cross-references: PDB:5XWU
Protein: DP04056 (UniProt Q96NI6)
Region: residues 222	to 231
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Ten
residues between the seventh and eighth repeats were disordered.
Cross-references: PDB:5XWT
Protein: DP04056 (UniProt Q96NI6)
Region: residues 292	to 378
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the apo-SALM5 structure,
the electron density of the Ig domain was mostly invisible,
probably owing to the structural disorder.
Cross-references: PDB:5XWS
Protein: DP04056 (UniProt Q96NI6)
Region: residues 292	to 378
Annotation: disorder to order (Structural transition)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron densities
of the Ig domains of SALM2 and SALM5 became relatively clear
upon binding to PTPδ, suggesting that the Ig domains of SALM2
and SALM5 were partly stabilized by the interaction with PTPδ.
Cross-references: PDB:5XWS
PDB:5XWT
Protein: DP04057 (UniProt Q8BPQ7)
Region: residues 390	to 413
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 254–424 of RUTBC2 RBD are well
defined except for the loop before the last ß strand (residues
390–413).
Cross-references: PDB:4QXA