LiteFold/DisProt huggingface dataset:
Protein: DP01024 (UniProt P27708)
Region: residues 1822	to 1846
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The last 25 amino acids of the C-terminal extension (residues 1822–1846) are not seen in the electron density maps, and likely belong to the linker sequence connecting with the ATCase domain of CAD.
Cross-references: PDB:4C6J
PDB:4C6C
PDB:4C6F
PDB:4BY3
PDB:4C6I
PDB:4C6M
PDB:4C6B
PDB:4C6Q
PDB:4C6O
PDB:4C6N
PDB:4C6L
PDB:4C6P
PDB:4C6D
PDB:4C6K
PDB:4C6E
Protein: DP01024 (UniProt P27708)
Region: residues 1822	to 1846
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The last 25 amino acids of the C-terminal extension (residues 1822–1846) are not seen in the electron density maps, and likely belong to the linker sequence connecting with the ATCase domain of CAD.
This extension is an important structural component that fastens the bottom elements of the catalytic barrel and fixes the exit point of the linker that connects with the ATCase domain.
Cross-references: PDB:4C6J
PDB:4C6C
PDB:4C6F
PDB:4BY3
PDB:4C6I
PDB:4C6M
PDB:4C6B
PDB:4C6Q
PDB:4C6O
PDB:4C6N
PDB:4C6L
PDB:4C6P
PDB:4C6D
PDB:4C6K
PDB:4C6E
Protein: DP01026 (UniProt A5YV76)
Region: residues 1975	to 1990
Annotation: disorder to order (Structural transition)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Loops in the vicinity of the active site cleft are disordered in the apo form of mFAS and become stabilized upon cofactor binding. This includes residues 1975 to 1990, corresponding to the β4/α4 loop in FabG, that are presumably stabilized by interactions of Met1973 with the active site Lys1995, and part of the substrate binding extension (residues 2072 to 2075)
Cross-references: PDB:2VZ9
PDB:2VZ8
Protein: DP01026 (UniProt A5YV76)
Region: residues 2112	to 2512
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Bound NADP+ cofactors and the attachment sites for the disordered C-terminal ACP/TE domains
The flexibly tethered ACP and the following TE domains are not visualized in the structure.
Here, we present the crystal structure of mFAS in its free and NADP+-bound states, in which the flexibly tethered C-terminal ACP/TE domains (23) remain unresolved.
Cross-references: PDB:2VZ9
PDB:2VZ8
Protein: DP01027 (UniProt Q4DRC4)
Region: residues 210	to 241
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Both subunits have disordered C-termini and the lack of clear density prohibits tracing the chain further, thus the proposed cleavage site for this fragment of the enzyme cannot be visualized in this structure.
Cross-references: PDB:1TC1
Protein: DP01027 (UniProt Q4DRC4)
Region: residues 220	to 241
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Herein, we describe how limited proteolysis of the recombinant trypanosomal HPRT provided a new crystal form that yielded very high resolution X-ray diffraction data and permitted the solution of the crystal structure and refinement to 1.4 Å resolution [13]. 
 In addition to indicating that the start methionine had been removed from the recombinant enzyme, the data shows that the smaller molecular mass polypeptide observed in the SDS-PAGE was likely to be a product of cleavage by an endo-peptidase near the C-terminus of the recombinant HPRT.
Protein: DP01028 (UniProt Q59471)
Region: residues 1	to 45
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
The initial model including cobalamin was built with XFIT [[41]] to the experimental electron-density map at 2.5 Å resolution, except for residues as follows: residues 1–4 of the α subunit, residues 1–46 of the β subunit, residues 1–37 of the γ subunit, and a few residues located in the C terminus in all subunits.
The missing region in the β or γ subunits is shown in gray.
The N-terminal region up to Aspβ45 could not be located in the electron-density map. It was confirmed that this region had also been eliminated by limited proteolysis during crystallization.
Protein: DP01029 (UniProt Q59472)
Region: residues 1	to 36
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
The initial model including cobalamin was built with XFIT [[41]] to the experimental electron-density map at 2.5 Å resolution, except for residues as follows: residues 1–4 of the α subunit, residues 1–46 of the β subunit, residues 1–37 of the γ subunit, and a few residues located in the C terminus in all subunits. 
The missing region in the β or γ subunits is shown in gray.
In the γ subunit, the N-terminal region up to Argγ36 could not be located on the electron-density map. It was confirmed by SDS (sodium dodecyl sulfate)–polyacrylamide gel electrophoresis that this region had been removed by limited proteolysis during crystallization.
Protein: DP01031 (UniProt Q99IB8)
Region: residues 2224	to 2317
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 1H,15N HSQC of NS5A-D2 (Fig. 2A) displays a narrow proton chemical shift range, limited to 1 ppm excluding three outlying peaks (Trp312, Ala313, and Arg326; see below). This low level of dispersion again points to the nonstructured nature of the polypeptide, at least when isolated in solution.
Cross-references: BMRB:16165
Protein: DP01031 (UniProt Q99IB8)
Region: residues 2224	to 2317
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
In gel filtration chromatography, the protein elutes at a volume corresponding to a ∼30-kDa globular protein, (Fig. 1B). Such a large apparent molecular weight in a gel filtration assay is commonly associated with natively unfolded proteins devoid of globular domain (52).
Protein: DP01031 (UniProt Q99IB8)
Region: residues 2224	to 2317
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In aqueous buffer, NS5A-D2 gave a complex spectrum with a large negative band around 198 nm and a shoulder in the 220–240 nm range, indicating a mixture of random coil structure with the presence of some poorly defined structures.
Protein: DP01031 (UniProt Q99IB8)
Region: residues 2224	to 2317
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
Despite an excellent agreement between expected (11,639 Da) and experimental mass as determined by mass spectroscopy, NS5A-D2 has an apparent molecular weight of ∼18 kDa by SDS-PAGE. This discrepancy is probably due to the primary aa sequence of NS5A-D2, which includes many acidic residues and prolines (50, 51).
This abnormal behavior is observed in intrinsically disordered regions or IDPs.
Protein: DP01031 (UniProt Q99IB8)
Region: residues 2224	to 2317
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
To quantify the interaction strength between both partners, we titrated increasing amounts of unlabeled NS5A-D2 into samples of 15N-labeled CypA or CypB. Chemical shift changes of residues at the periphery of the binding site varied in a monotonous way from their free position toward the ligand saturated value, allowing the determination of KD values of 64 and 90 μm for CypA and CypB, respectively (Fig. 4, A–C).
Chemical shift perturbation experiments on both NS5A-D2·CypA and NS5A-D2·CypB complexes gave evidence for a direct physical interaction that is localized to the active site on the cyclophilins (Fig. 3).
Protein: DP01031 (UniProt Q99IB8)
Region: residues 2331	to 2440
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
Although the molecular mass of NS5A-D3 (JFH-1) was 11,837 Da, as determined by mass spectroscopy, the purified protein migrates as a ∼27-kDa protein by SDS-PAGE (Fig. 2A).
This abnormal behavior is observed in intrinsically disordered regions or IDPs.
Protein: DP01031 (UniProt Q99IB8)
Region: residues 2331	to 2440
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In conclusion, in aqueous buffer, NS5A-D3 (JFH-1) is mostly unfolded but has a short and stable α-helical secondary structure element centered around the N-terminal Ala367.
Both the narrow amide proton dispersion and the clustering of glycine and serine/threonine resonances confirm the non-structured nature of NS5A-D3 (JFH-1).
Cross-references: BMRB:16798
Protein: DP01031 (UniProt Q99IB8)
Region: residues 2331	to 2440
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectrum of NS5A-D3 is typical for a poorly folded protein with a large negative peak centered at 198 nm.
Protein: DP01031 (UniProt Q99IB8)
Region: residues 2331	to 2440
Annotation: protein binding (Molecular function)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
 By comparison with the NS5A-D3 spectra recorded alone, we identified the residues involved in interaction with CypA based on chemical shift perturbations and/or peak broadening. Most of the perturbed resonances belong to residues in the C-terminal half of NS5A-D3 (from Ser415 to Asp461 for JFH-1 and from Ser414 to Val445 for Con1) (Fig. 1).
Protein: DP01031 (UniProt Q99IB8)
Region: residues 2226	to 2238
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Based on our previous assignment of the NS5A-D2 spectrum, we could plot on a per residue basis the ratio of the peak intensities in the absence or presence of NS5BΔ21, and as such identified three different regions of NS5A-D2 that interact with the polymerase (Fig. 1, A and C, and supplemental Fig. 5). Two peptides of roughly 10 residues form the first anchoring points (residues 250–262 (region A) and residues 274–287 (region B)). A larger zone of interaction spanning residues 306–333 forms the third zone of interaction (region C).
The 250-262 residues from NS5A protein corresponds to the 2226-2238 region of the Hepatitis C virus genotype 2a (isolate JFH-1) genome polyprotein. The binding partner, NS5BΔ21, is also encoded in the polyprotein within the residues 2464-3033
Protein: DP01031 (UniProt Q99IB8)
Region: residues 2250	to 2263
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Based on our previous assignment of the NS5A-D2 spectrum, we could plot on a per residue basis the ratio of the peak intensities in the absence or presence of NS5BΔ21, and as such identified three different regions of NS5A-D2 that interact with the polymerase (Fig. 1, A and C, and supplemental Fig. 5). Two peptides of roughly 10 residues form the first anchoring points (residues 250–262 (region A) and residues 274–287 (region B)). A larger zone of interaction spanning residues 306–333 forms the third zone of interaction (region C).
The 274-287 residues from NS5A protein corresponds to the 2250-2263 region of the Hepatitis C virus genotype 2a (isolate JFH-1) genome polyprotein. The binding partner, NS5BΔ21, is also encoded in the polyprotein within the residues 2464-3033
Protein: DP01031 (UniProt Q99IB8)
Region: residues 2282	to 2309
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Based on our previous assignment of the NS5A-D2 spectrum, we could plot on a per residue basis the ratio of the peak intensities in the absence or presence of NS5BΔ21, and as such identified three different regions of NS5A-D2 that interact with the polymerase (Fig. 1, A and C, and supplemental Fig. 5). Two peptides of roughly 10 residues form the first anchoring points (residues 250–262 (region A) and residues 274–287 (region B)). A larger zone of interaction spanning residues 306–333 forms the third zone of interaction (region C).
The 306-333 residues from NS5A protein corresponds to the 2282-2309 region of the Hepatitis C virus genotype 2a (isolate JFH-1) genome polyprotein. The binding partner, NS5BΔ21, is also encoded in the polyprotein within the residues 2464-3033
Protein: DP01031 (UniProt Q99IB8)
Region: residues 2224	to 2317
Annotation: protein binding (Molecular function)
Evidence: surface plasmon resonance evidence used in manual assertion
Supporting statements:
Analysis of the corresponding sensorgrams showed that the signal response at equilibrium was initially dose-dependent and then saturated, which corresponds to a specific interaction between NS5A-D2 and NS5BΔ21. The Scatchard plot of these data is linear, and thus data are consistent with the Langmuir model (see supplemental Fig. 3). The measured association (ka) and dissociation (kd) rate constants allowed the determination of an equilibrium dissociation constant (KD) of 21 × 10−6 m (see Fig. 2) for the interaction between NS5BΔ21 and NS5A-D2.
Protein: DP01031 (UniProt Q99IB8)
Region: residues 2280	to 2299
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In agreement with our previous findings (53) and confirmed very recently with a peptide-immobilized spot assay (69), two different regions of NS5A-D2 were broadened in the presence of CypA (Fig. 1D). The first comprises residues Gly-304–Pro-323, whereas the second corresponds to residues Gly-337–Pro-341 located at the C-terminal end.
The 304-323 residues from NS5A protein corresponds to the 2280-2299 region of the Hepatitis C virus genotype 2a (isolate JFH-1) genome polyprotein.
Protein: DP01031 (UniProt Q99IB8)
Region: residues 2313	to 2317
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In agreement with our previous findings (53) and confirmed very recently with a peptide-immobilized spot assay (69), two different regions of NS5A-D2 were broadened in the presence of CypA (Fig. 1D). The first comprises residues Gly-304–Pro-323, whereas the second corresponds to residues Gly-337–Pro-341 located at the C-terminal end.
The 337-341 residues from NS5A protein corresponds to the 2313-2317 region of the Hepatitis C virus genotype 2a (isolate JFH-1) genome polyprotein.
Protein: DP01032 (UniProt Q06556)
Region: residues 848	to 969
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
The absence of fixed long-distance intramolecular interactions is confirmed by the results of unfolding experiments monitored by gel-permeation chromatography.
Protein: DP01032 (UniProt Q06556)
Region: residues 848	to 969
Annotation: disorder (Structural state)
Evidence: fluorescence anisotropy evidence used in manual assertion
Supporting statements:
It was determined that ANS did not bind to rFNBD-A or rFNBD-B under any conditions tested, indicating that the proteins do not appear to be capable of forming localized, stable regions of hydrophobic side chains (data not shown). From the experimental evidence presented above we conclude that the rFNBDs do not have the characteristics of folded or partially folded (i.e. a molten globule) proteins, instead the structure of the repeat regions is highly dynamic and appears to be thermodynamically indistinct from the denatured state.
Protein: DP01032 (UniProt Q06556)
Region: residues 806	to 969
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
This type of spectra is characteristic of proteins that are predominately composed of random coil and γ-turns and contain a minimum amount of α-helix or β-sheet conformation(15., 16.). A larger version of the FnbA Fn binding segment, PAQ8(9.), contains A1, A2, and A3 as well as an upstream sequence designated Au (Fig. 1A). This sequence is similar to the other Fn binding motifs (Fig. 1B) and has been shown to have Fn binding activity. PAQ8, when analyzed by far-UV CD, appears to have no significant increase in secondary structure over the smaller proteins (Fig. 2).
Protein: DP01032 (UniProt Q06556)
Region: residues 848	to 969
Annotation: fibronectin binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
On addition of N29 to rFNBD-A at ratios ranging from 0:1 to 4.9:1 there is a marked change in the appearance of the far-UV CD spectra.
Protein: DP01039 (UniProt Q85258)
Region: residues 336	to 523
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 1H NMR spectra recorded under these different conditions were quite similar and showed a relatively poor dispersion of the amide protons in the 6–9 ppm region (Fig. 6A), characteristic of a rather unfolded protein. However, several aliphatic peaks were observed at ∼0 ppm, located away from the random coil frequency at ∼0.7 ppm of the main peak.
These values of λNOE are characteristic of partially unfolded or degraded proteins (32). Because the VPg samples were found not to be degraded after the NMR experiment (data not shown), these data confirm that VPg is in an unfolded state.
Protein: DP01039 (UniProt Q85258)
Region: residues 336	to 523
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectra of monomeric and dimeric VPg (Fig. 5A) are identical and exhibit negative ellipticity near 205 nm, a shoulder at 220 nm, and a weak positive maximum of ∼190 nm.
The effect of temperature was tested (Fig. 5B), and in common with other unfolded proteins (43), no cooperative transition of the molar ellipticity was observed. Our data show that VPg does not have a compact structure, nor does it contain significant secondary elements.
Protein: DP01039 (UniProt Q85258)
Region: residues 336	to 523
Annotation: disorder (Structural state)
Evidence: analytical ultracentrifugation evidence used in manual assertion
Supporting statements:
The results thus imply an elongated structure for both monomeric and dimeric VPg.
Protein: DP01039 (UniProt Q85258)
Region: residues 336	to 523
Annotation: disorder (Structural state)
Evidence: dynamic light scattering assay evidence used in manual assertion
Supporting statements:
The dynamic light scattering technique makes it possible to monitor unfolding or denaturation caused by changes in pH or temperature. The protein melting point temperature Tm obtained from dynamic light scattering analysis is indicative of thermal stability.
Protein: DP01039 (UniProt Q85258)
Region: residues 336	to 523
Annotation: protein homodimerization activity (Molecular function)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
When VPg was prepared under nonreducing conditions and run on semi-denaturing SDS-PAGE, a slowly migrating band of 44 kDa, consistent with the molecular weight calculated for VPg dimer (21) was observed in addition to a major band (22kDa) corresponding to the monomeric protein (Fig. 3A, lane 1).
Protein: DP01039 (UniProt Q85258)
Region: residues 336	to 523
Annotation: protein homodimerization activity (Molecular function)
Evidence: analytical ultracentrifugation evidence used in manual assertion
Supporting statements:
The results of the monomer/dimer mixture analysis gives the s20,w values 1.7 and 3.0 S for VPg monomer and dimer, respectively.
Protein: DP01043 (UniProt Q80FJ1)
Region: residues 2	to 31
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
From NMR spectroscopic data and simulated annealing, the soluble nonmyristoylated p14 ectodomain peptide consists of an N-proximal extended loop flanked by two proline hinges. The remaining two-thirds of the ectodomain peptide structure is disordered, consistent with predictions based on CD spectra of the myristoylated peptide
Protein: DP01043 (UniProt Q80FJ1)
Region: residues 2	to 31
Annotation: flexible N-terminal tail (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The C-terminal disordered region (residues 15–31) may act as a flexible linker, facilitating conformational changes in either the structure or spatial arrangement of the p14 HP, similar to the proposed role of the
linker region that connects the influenza HA fusion peptide to the remainder of the HA2 polypeptide
Protein: DP01043 (UniProt Q80FJ1)
Region: residues 2	to 31
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Solution NMR spectroscopy was used to provide additional insight into why residues clustered near the central portion of the p14 HP exert a sequence-specific effect on p14 fusion activity, while at the same time CD analysis predicts the p14 ectodomain is mostly disordered
Protein: DP01043 (UniProt Q80FJ1)
Region: residues 2	to 31
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Circular dichroism (CD) of a myristoylated peptide representing the majority of the p14 ectodomain suggested this region is mostly disordered in solution but assumes increased structure in an apolar environment
Protein: DP01043 (UniProt Q80FJ1)
Region: residues 2	to 31
Annotation: lipid binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The inherent structural plasticity of many fusion peptides is likely essential for their role as membrane destabilizing modules. We propose that the p14 HP is no exception, requiring a dynamic structure in addition to a potential membrane-embedding loop in order to achieve maximal function as a membrane-
destabilizing module.
Protein: DP01044 (UniProt Q47785)
Region: residues 82	to 103
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
However, the absence of a single main chain conformation of the C-terminal part inthe structure of Se-Met-EntA-im-(L31M+L80M) and that of molecule B points to a flexible C terminus.
Cross-references: PDB:2BL8
Protein: DP01049 (UniProt Q6QCC2)
Region: residues 41	to 51
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The latter interactions define the conformation of a long loop (segment 22–32), which is completely solvent-exposed and rich in charged residues.
The segment 22-32 is corresponding to 41-51 in UniProt.
Cross-references: BMRB:16058
PDB:2KC0