LiteFold/DisProt huggingface dataset:
Protein: DP00179 (UniProt P01094)
Region: residues 2	to 34
Annotation: endopeptidase inhibitor activity (Molecular function)
Evidence: in vitro cleavage assay evidence used in manual assertion
Supporting statements:
The recombinant wild type protein inhibited yeast proteinase A effectively at pH 3.1 (Table 1), and its potency increased even further at higher pH values.
. A synthetic peptide spanning residues 2–34 of IA3 also showed a potency comparable to that of the full-length protein inhibitor, as measured by Ki values (Table 1). This suggests that the initiator Met residue and residues 35–68 in the IA3 sequence19 are not important for inhibitory function. Peptides 2–15 and 16–34 did not inhibit the enzyme when added either alone or together.
Thus, a contiguous stretch of residues from 2–34 not only prevents cleavage of this peptide by proteinase A but also acts an effective inhibitor of the enzyme.
Protein: DP00180 (UniProt P19972)
Region: residues 146	to 222
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
SMK toxin is a killer toxin produced by a halotolerant yeast, Pichia farinosa. It is a heterodimer consisting of α (63 aa) and β (77 aa) subunits, between which no disulfide bond exists. The two subunits interact tightly with each other below pH 5. However, the subunits dissociate under neutral conditions, resulting in the aggregation of the α subunit and the concomitant loss of killer activity. CD spectral measurements showed that the secondary structure of the SMK toxin changes drastically in the pH range 5.1–5.5 and that after the dissociation of the subunits, the soluble βsubunit alone cannot take any secondary structure.
After removing theαsubunit from the turbid solution at pH 7.0 by centrifugation, the soluble β subunit gives a CD spectrum which is identical with that of a peptide in the random coil (Figure 1). This result clearly indicates that the β subunit cannot take any secondary structure in the absence of the α subunit.
The α and β subunits consist of amino acid residues 19-81 and 146-222, as previously described in PMID:8300637
Protein: DP00180 (UniProt P19972)
Region: residues 146	to 222
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
SMK toxin is a killer toxin produced by a halotolerant yeast, Pichia farinosa. It is a heterodimer consisting of alpha (63 aa) and beta (77 aa) subunits, between which no disulfide bond exists. The two subunits interact tightly with each other below pH 5. However, the subunits dissociate under neutral conditions, resulting in the aggregation of the alpha subunit and the concomitant loss of killer activity. CD spectral measurements showed that the secondary structure of the SMK toxin changes drastically in the pH range 5.1-5.5 and that after the dissociation of the subunits, the soluble beta subunit alone cannot take any secondary structure.
Protein: DP00180 (UniProt P19972)
Region: residues 146	to 222
Annotation: protein binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The crystal structure of the SMK toxin indicates that about 60% of the surface of the β subunit comprises hydrophobic residues, that almost all of hydrophobic residues of the β subunit are involved with the interactions with the α subunit and that four pairs of acidic residues, i.e. Asp76(β4)–Asp213(L6),Asp161(L4)–Asp195(β4),Glu158(L4)–Asp222(L6)andAsp199(β5)–Asp222(L6), exist, in each of which the distance between the carboxyl groups is sufficiently short for the formation of hydrogen bonds (Figure 2).
Protein: DP00180 (UniProt P19972)
Region: residues 146	to 222
Annotation: toxin sequestering activity (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In a previous paper (Suzuki and Nikkuni, 1994), we suggested that the inactivation of the SMK toxin at neutral pH is caused by the dissociation of the two subunits. The CD analyses described here clearly indicate that the structure of the SMK toxin changes under such conditions.
Protein: DP00181 (UniProt P08775)
Region: residues 1529	to 1959
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectrum in water resembles that of an essentially unordered peptide, with a strong negative band at 197 nm.
Protein: DP00182 (UniProt P03087)
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:
We note three regions in which the electron density is poorly defined. The first encompasses the N-terminal 13 amino acid residues, which are not visible at all. This part of the monomer is probably disordered, and it is not contained in our model.
Cross-references: PDB:1SVA
Protein: DP00182 (UniProt P03087)
Region: residues 344	to 362
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The C-terminal 6 residues of VP1 monomers α and α″ and the C-terminal 18 residues of β are disordered and excluded from the model presented here.
Cross-references: PDB:1SVA
Protein: DP00182 (UniProt P03087)
Region: residues 1	to 21
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
A DNA-binding domain (DBD) was identified on simian virus 40 (SV40) major capsid protein Vp1, and the domain's function in the SV40 life cycle was examined. The N-terminal location of the DBD is consistent with the crystallographic structure of the virion in which the Vp1 N terminus is oriented toward the minichromosomal core and is disordered. [extracts from abstract and discussion]
Cross-references: PDB:1SVA
Protein: DP00182 (UniProt P03087)
Region: residues 1	to 21
Annotation: molecular adaptor activity (Molecular function)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
Collective results support a role for Vp1 NLS2-DBD2 in the assembly of virion particles. The results also suggest that this determinant can function in the infection of new cells.
Protein: DP00184 (UniProt P11473)
Region: residues 165	to 215
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
The radii of gyration (Table 1) of VDRwt and VDRmt complexed to 1,25(OH)2D3 are 26.2 and 23.4 Å, respectively. The difference of 2.8 Å observed between the radii of gyration of the two proteins corresponds to an increase in volume of 35% for a spherical object. A similar difference (2.2 Å) has been observed by small angle neutron scattering (data not shown) between VDRwt and VDRmt. This difference is rather large and suggests a disordered insertion domain.
The difference of 15 Å between the Dmax values of VDRmt and VDRwt is rather large for an additional domain of 50 residues, suggesting that this insertion domain is not well ordered and may adopt several conformations in solution.
Protein: DP00186 (UniProt Q95V77)
Region: residues 1	to 143
Annotation: disorder (Structural state)
Evidence: Fourier-transform infrared spectroscopy evidence used in manual assertion
Supporting statements:
FT-IR spectra collected from soluble AavLEA1 samples in 2H2O show an amide I pattern indicative of a mainly disordered polypeptide (Fig. 7A), in agreement with CD data. Second derivative analysis of the amide I band showed two main peaks at 1644 cm−1 and 1667 cm−1, characteristic of random coil structures (42).
Protein: DP00186 (UniProt Q95V77)
Region: residues 1	to 143
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
However, significant defined secondary structure was not detected for AavLEA1; signatures of α-helix and β-sheet were absent, with the spectrum showing instead that the protein is most likely unstructured through a temperature range of 4 to 75 °C (Fig.5).
Protein: DP00186 (UniProt Q95V77)
Region: residues 1	to 143
Annotation: disorder (Structural state)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
The single tryptophan residue in AavLEA1, at position 49 of 162 (allowing for the His tag, position 30 of 143 in the native nematode sequence; Fig. 1), gives rise to a λmax at 4 °C of 355 nm, which is indicative of a solvent-exposed side chain (Fig. 6).
Protein: DP00186 (UniProt Q95V77)
Region: residues 1	to 143
Annotation: disorder (Structural state)
Evidence: gel-filtration evidence used in manual assertion
Supporting statements:
The Stokes' radius (Rs sed) of AavLEA1 was calculated from sedimentation analysis to be 3.91 nm. This is larger than expected if AavLEA1 were globular in structure but is consistent with it being an extended or highly swollen protein.
The gel filtration column was calibrated using globular proteins with known Rsas standards, allowing Rs gel for AavLEA1 to be estimated at 3.38 nm. This is somewhat lower than the value obtained from ultracentrifugation, possibly because of matrix interaction effects, but is still far in excess of the expectedRs value for a globular protein of similar mass and supports the model of AavLEA1 having low compactness.
Protein: DP00187 (UniProt P04273)
Region: residues 23	to 106
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Two dimensional 1H/15N correlation (HSQC) 50 NMR spectra collected on hamster PrP 23–106 both with and without PPS exhibited limited chemical shift dispersion (~ 1 ppm), consistent with extensive conformational averaging and a lack of well defined, compact structure (Figure 1).
The majority of chemical shifts of backbone and sidechain atoms were close to random coil values, consistent with the disordered nature of PrP 23–106 58.
Cross-references: PDB:2KKG
Protein: DP00187 (UniProt P04273)
Region: residues 90	to 126
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Essentially three parts to the protein are readily reflected in simple NMR spectral features: residues 90–112 are characterized by narrow (18 Hz) 15N heteronuclear single quantum coherence (HSQC) spectral signals and few long-range NOE crosspeaks; residues 113–126 have relatively narrow (ca. 18 Hz) 15N HSQC spectral (ca. 18Hz) signals and many NOE crosspeaks; and most of the remaining residues exhibit ca. 6 Hz broader HSQC signals and numerous NOE crosspeaks.
Cross-references: PDB:1B10
Protein: DP00187 (UniProt P04273)
Region: residues 90	to 122
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows that this region lacks electron density, indicating that it is disordered.
Cross-references: PDB:4YXL
Protein: DP00187 (UniProt P04273)
Region: residues 23	to 106
Annotation: disorder (Structural state)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
The fluorescence spectrum of PrP 23–106 exhibited a maximum around 356 nm indicating that the aromatic residues are exposed to the aqueous solvent (Figure 5(a)).
Protein: DP00187 (UniProt P04273)
Region: residues 23	to 106
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
An isodichroic point at ~206–208 nm indicated a β-turn/PPII conformational transition 67, 68, consistent with the β-turn conformation detected by NMR without PPS (described above) and earlier studies of N-terminal PrP fragments, in which PPII and β-turn conformations were recognized 40–43.
The pentosan polysulfate (PPS) is one of the most potent anti-prion.
Protein: DP00187 (UniProt P04273)
Region: residues 23	to 106
Annotation: amyloid fibril formation (Biological process)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
An isodichroic point at ~206–208 nm indicated a β-turn/PPII conformational transition 67, 68, consistent with the β-turn conformation detected by NMR without PPS (described above) and earlier studies of N-terminal PrP fragments, in which PPII and β-turn conformations were recognized 40–43.
The pentosan polysulfate (PPS) is one of the most potent anti-prion.
These findings indicated that addition of PPS to PrP 23–106 enhanced the latter’s β-turn component, again consistent with NMR data.
Protein: DP00187 (UniProt P04273)
Region: residues 23	to 106
Annotation: amyloid fibril formation (Biological process)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In contrast, NMR spectra recorded on free PrP 23–106 (i.e. no PPS) but otherwise under identical sample conditions (i.e. buffer/20% DMSO) revealed large differences with NMR spectra acquired on the PrP 23–106/PPS complex.
The pentosan polysulfate (PPS) is one of the most potent anti-prion.
The 3D 15N-edited 1H-1H NOESY spectrum acquired on PrP 23–106 without PPS exhibited far fewer NOE cross-peaks for the octarepeat residues.
Protein: DP00187 (UniProt P04273)
Region: residues 23	to 106
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In contrast, NMR spectra recorded on free PrP 23–106 (i.e. no PPS) but otherwise under identical sample conditions (i.e. buffer/20% DMSO) revealed large differences with NMR spectra acquired on the PrP 23–106/PPS complex.
The pentosan polysulfate (PPS) is one of the most potent anti-prion.
The 3D 15N-edited 1H-1H NOESY spectrum acquired on PrP 23–106 without PPS exhibited far fewer NOE cross-peaks for the octarepeat residues.
Protein: DP00188 (UniProt P12359)
Region: residues 1	to 88
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 spinach PSII-LHCII supercomplex, shows this region lacks electron density, indicating it is disordered.
Cross-references: EMDB:6617
PDB:3JCU
Protein: DP00189 (UniProt P04324)
Region: residues 42	to 57
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Here, we investigate the solution structures of the myristoylated and non-myristoylated HIV-1 Nef anchor domain (2–57) under buffer conditions as close to physiological conditions as possible.
The structure of the domain was studied under nearly physiological conditions in aqueous solution; the experimental data show that the isolated domain is not compactly folded and does not have a unique structure. The only canonic secondary structure element found in the non-myristyolated anchor domain is a short α-helical element (helix H2) from Arg35 to Gly41 (Figure 4).
Cross-references: PDB:1QA5
PDB:1QA4
Protein: DP00189 (UniProt P04324)
Region: residues 2	to 14
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Here, we investigate the solution structures of the myristoylated and non-myristoylated HIV-1 Nef anchor domain (2–57) under buffer conditions as close to physiological conditions as possible.
Myristoylation induces a change of the conformational states of the anchor domain, leading to the stabilization of helix H2 and to the induction of the first helical element H1 (Pro14 to Arg22).
Cross-references: PDB:1QA5
Protein: DP00189 (UniProt P04324)
Region: residues 2	to 34
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The structure of the domain was studied under nearly physiological conditions in aqueous solution; the experimental data show that the isolated domain is not compactly folded and does not have a unique structure. The only canonic secondary structure element found in the non-myristyolated anchor domain is a short α-helical element (helix H2) from Arg35 to Gly41 (Figure 4). 
Cross-references: PDB:1QA4
PDB:1QA5
Protein: DP00189 (UniProt P04324)
Region: residues 2	to 14
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Here, we investigate the solution structures of the myristoylated and non-myristoylated HIV-1 Nef anchor domain (2–57) under buffer conditions as close to physiological conditions as possible.
Myristoylation induces a change of the conformational states of the anchor domain, leading to the stabilization of helix H2 and to the induction of the first helical element H1 (Pro14 to Arg22).
Cross-references: PDB:1QA5
PDB:1QA4
Protein: DP00189 (UniProt P04324)
Region: residues 2	to 14
Annotation: fatty acylation display site (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Myristoylation induces a change of the conformational states of the anchor domain, leading to the stabilization of helix H2 and to the induction of the first helical element H1 (Pro14 to Arg22).
Cross-references: PDB:1QA5
Protein: DP00190 (UniProt P38038)
Region: residues 52	to 62
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The well-folded domain consists of residues 63−208, whereas residues 52−62 and 209−218, which were present in the molecular construct, are disordered. 
Cross-references: PDB:1YKG
Protein: DP00190 (UniProt P38038)
Region: residues 209	to 218
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The well-folded domain consists of residues 63−208, whereas residues 52−62 and 209−218, which were present in the molecular construct, are disordered. 
Cross-references: PDB:1YKG
Protein: DP00192 (UniProt P02668)
Region: residues 1	to 190
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The far-UV circular dichroic spectra of κ-casein at different pH and concentration of CTAB have been shown in Fig. 9.
The far-UV circular dichroic spectra shows a large negative ellipticity at 200 nm and moderate ellipticity at 190 nm, indicating it is disordered.
Protein: DP00194 (UniProt P0AFZ3)
Region: residues 111	to 165
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
The proteolytic sensitivity, variable length, and poor sequence conservation of the C-terminal residues of SspB suggest that this region (residues 111–165 in E. coli SspB) might be unstructured.
Protein: DP00194 (UniProt P0AFZ3)
Region: residues 118	to 165
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Indeed, the circular-dichroism (CD) spectrum of residues 118 to 165 in intact E. coli SspB (Figure 2B, inset; determined by subtracting the spectrum for the 1–117 fragment from the spectrum of the intact protein) had a minimum at 198 nm, as would be expected if the C-terminal 48 residues of E. coli SspB form an ensemble of random-coil conformations (Ausio et al. 1987).
Protein: DP00194 (UniProt P0AFZ3)
Region: residues 112	to 154
Annotation: flexible linker (Disorder function)
Evidence: mutant phenotype evidence used in manual assertion
Supporting statements:
To create a more dramatic change in the length of the linker, we deleted residues 112–154, leaving approximately eight residues between Tyr110, the last fully-structured residue in the substrate binding domain (Levchenko et al. 2003), and the conserved sequence in the XB module. As shown in Figure 5 (experiment k), this mutant protein was also able to stimulate degradation, but only about 60% as well as full-length SspB. These experiments show that large variations in the composition and length of the linker can be tolerated with retention of substantial SspB activity, but also suggest that sufficient length or linker flexibility is required for full SspB function.
Protein: DP00194 (UniProt P0AFZ3)
Region: residues 156	to 165
Annotation: positive regulation of proteolysis involved in cellular protein catabolic process (Biological process)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
Full-length E. coli SspB (1–165) stimulates ClpXP-mediated degradation of GFP-ssrA (Levchenko et al. 2000, Flynn et al. 2001). By contrast, neither the purified proteolytic fragment containing the SspB substrate binding domain (1–117) nor the substrate binding domain plus linker (1–155) enhanced ClpXP-degradation of GFP-ssrA (Figure 1C). Thus, residues at the extreme C terminus of SspB are required, either directly or indirectly, for this protein to stimulate ClpXP of degradation ssrA-tagged substrates.
Protein: DP00194 (UniProt P0AFZ3)
Region: residues 156	to 165
Annotation: positive regulation of ATP-dependent activity (Biological process)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
Full-length E. coli SspB (1–165) stimulates ClpXP-mediated degradation of GFP-ssrA (Levchenko et al. 2000, Flynn et al. 2001). By contrast, neither the purified proteolytic fragment containing the SspB substrate binding domain (1–117) nor the substrate binding domain plus linker (1–155) enhanced ClpXP-degradation of GFP-ssrA (Figure 1C). Thus, residues at the extreme C terminus of SspB are required, either directly or indirectly, for this protein to stimulate ClpXP of degradation ssrA-tagged substrates.
Protein: DP00194 (UniProt P0AFZ3)
Region: residues 118	to 165
Annotation: molecular adaptor activity (Molecular function)
Evidence: gel-filtration evidence used in manual assertion
Supporting statements:
Gel-filtration experiments showed that the C-terminal residues of SspB are also required for formation of stable delivery complexes with ssrA-tagged substrates and ClpX. As expected (Wah et al. 2002), incubation of GFP-ssrA, full-length SspB, and ClpX resulted in formation of a stable ternary complex (Figure 3, top trace). By contrast, when the isolated substrate binding domain was substituted for full-length SspB, no delivery complex was observed, and all of the GFP-ssrA migrated at a position expected for a complex of a dimer of the substrate binding domain with two molecules of GFP-ssrA (Figure 3, bottom trace).
ssrA tag contains the sequence AANDENYALAA.
Protein: DP00194 (UniProt P0AFZ3)
Region: residues 156	to 165
Annotation: protein binding (Molecular function)
Evidence: fluorescence anisotropy evidence used in manual assertion
Supporting statements:
A synthetic BODIPY-labeled peptide containing the C-terminal 10 residues of SspB (156–165) bound ClpX with a Kd of 23 ± 5 μM (Figure 4A).
Protein: DP00194 (UniProt P0AFZ3)
Region: residues 156	to 165
Annotation: positive regulation of ATP-dependent activity (Biological process)
Evidence: spectrophotometry evidence used in manual assertion
Supporting statements:
The unlabeled XB peptide stimulated the ATPase activity of ClpX with a half-maximal value (19 ± 5 μM; Figure 4B) in good agreement with the Kd for binding. At saturation, the XB peptide stimulated the ATPase activity of ClpX by a factor of roughly 2-fold, a value similar to the stimulation observed with full-length SspB (Wah et al. 2002). By contrast, SspB fragments containing just the substrate binding domain or substrate binding plus linker regions showed no significant stimulation of ATPase activity (data not shown).