LiteFold/DisProt huggingface dataset:
Protein: DP00086 (UniProt P04637)
Region: residues 1	to 61
Annotation: self-inhibition (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Taken together, the NMR and fluorescence data suggest a model in which the p53 NTAD can inhibit binding to nontarget DNA but does not affect binding to a cognate recognition element.
Protein: DP00086 (UniProt P04637)
Region: residues 361	to 393
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In addition, all of the new resonance peaks observed in the p53 construct containing the C-terminal domain (Fig. 3b) appear at frequencies typical of unstructured amides (-8 p.p.m. in the proton dimension). This suggests that the C-terminal domain is not likely to be folded into regular secondary structure.
Protein: DP00086 (UniProt P04637)
Region: residues 361	to 393
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In contrast, the behavior of the C-terminal domain was best characterized as unstructured and highly mobile, with chemical shift values close to random coil.
Protein: DP00086 (UniProt P04637)
Region: residues 19	to 26
Annotation: ubiquitin protein ligase binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The position of the p53 helix allows Phe19, Trp23, and Leu26, which are aligned along its hydrophobic face, to insert deep inside the MDM2 cleft (Fig. 5A), and pack with the cleft in a complementary fashion (Fig. 5B).
In certain cancers, MDM2 amplification is a common event and contributes to the inactivation of p53.
In normal cells, MDM2 and p53 form a negative feedback loop that helps to limit the growth-suppressing activity of p53.
The region 19-26 corresponds to a destruction/degron motif that binds to the MDM2 E3 ubiquitin-protein ligase.
Cross-references: PDB:1YCR
ELM:deg_mdm2_1
Protein: DP00086 (UniProt P04637)
Region: residues 367	to 388
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Secondary structure content estimated by analysis of CD spectra for each of the thirteen IDRs showed that none contained more than two residues in a helical conformation (Figures 1-3, Table 3-5), which is insufficient for the formation of a stable α-helix requiring a minimum of six residues. Formation of a minimal beta-structure requires six residues [38], and seven of the thirteen IDRs (Table 3-5) appear to have between six to eight residues in extended or β-conformation which may be sufficient for forming short stable β-hairpins (Table 3-5). Thus, while none of the selected IDRs had stable helical structure, several may have short β-strands.
Protein: DP00086 (UniProt P04637)
Region: residues 1	to 93
Annotation: disorder (Structural state)
Evidence: near-UV circular dichroism evidence used in manual assertion
Supporting statements:
For Np53, signals in the near-UV region are largely missing. Under denaturing conditions (4 M GdmCl), no significant change in the near-UV CD signal of Np53 could be detected (Figure 2(C)). The low ellipticity values of the CD signal, together with the insensitivity to denaturation account for a solvent-exposed, unstructured protein.
Protein: DP00086 (UniProt P04637)
Region: residues 1	to 93
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The spectrum of the isolated NTD of p53 exhibits a minimum at 200 nm. The ΘMRW values above 200 nm suggest that α-helices and β-strands are largely missing. Far-UV CD spectra of Np53 analyzed under denaturing conditions (4 M GdmCl) showed only minor structural differences from spectra recorded under native conditions (Figure 2(A)). Taken together, the CD spectra indicate a remarkably high content of unstructured regions in Np53
Protein: DP00086 (UniProt P04637)
Region: residues 1	to 93
Annotation: disorder (Structural state)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
Spectra recorded under native as well as under denaturing conditions (4 M GdmCl) did not show significant changes in the maximum emission wavelength or the emission intensity (Figure 2(D)). The emission maximum of the standard N-acetyl-tryptophan-amide (Sigma) was 360 nm. Under native conditions, the fluorescence emission maximum of Np53 was 357 nm, under denaturing conditions 356 nm, both indicating complete solvent exposure. The existence of a well-defined tertiary structure could therefore be excluded
Protein: DP00086 (UniProt P04637)
Region: residues 1	to 93
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We observed small proton resonance dispersion in a spectral range of 7.5–8.7 ppm, characteristic for a highly unfolded protein. In addition, the seven NH2 side-chain signals of asparagine and glutamine residues accumulate in their characteristic random coil region of 7.59 ppm/6.88 ppm. The same was observed for the side-chain signals of the three tryptophan residues of Np53, which appear at 10.2 ppm. Taken together, the spectrum shows, at the level of amino acids, that residues 1–93 of p53 are mostly unstructured
Protein: DP00087 (UniProt P68336)
Region: residues 413	to 490
Annotation: disorder (Structural state)
Evidence: dynamic fluorescence quenching evidence used in manual assertion
Supporting statements:
Dynamic quenching constants for both GV-5HW442 and GV-5HW473 are thus of the same order of magnitude as that for free 5-OH-Trp. Consistent with the quenching study of GAL4-VP16 containing natural Trp(64), these results suggest that residues 442 and 473 are solvent-exposed.
GV-5HW442 and GV-5HW473 are in-frame fusions of GV to the VP16 activation domain (amino acids 413-490) with the incorporation of 5-hydroxytryptophan at position 442 or 473, respectively.
Protein: DP00087 (UniProt P68336)
Region: residues 413	to 490
Annotation: molecular function activator activity (Molecular function)
Evidence: dynamic fluorescence quenching evidence used in manual assertion
Supporting statements:
The presence of TBP altered the solvent accessibility of both residue 442 and 473. The downward curves of the Stern-Volmer plots were best fit to a two-species model, with approximately 40% of the probe molecules being inaccessible to acrylamide (assumed Ksv of 0) and an accessible fraction of approximately 60% having a Ka of 4.0 M-1 or 7.0 M-1 for GV-7AW442 or GV-7AW473, respectively." Results "However, TFIIB did alter the solvent accessibility of GV-7AW473. Its Stern-Volmer plot was downward curved; in a two-species model, approximately 30% of the probe was inaccessible, and the accessible fraction had a Ka of 4.9 M-1.
GV-5HW442 and GV-5HW473 are in-frame fusions of GV to the VP16 activation domain (amino acids 413-490) with the incorporation of 5-hydroxytryptophan at position 442 or 473, respectively.
Protein: DP00087 (UniProt P68336)
Region: residues 413	to 490
Annotation: protein binding (Molecular function)
Evidence: dynamic fluorescence quenching evidence used in manual assertion
Supporting statements:
The presence of TBP altered the solvent accessibility of both residue 442 and 473. The downward curves of the Stern-Volmer plots were best fit to a two-species model, with approximately 40% of the probe molecules being inaccessible to acrylamide (assumed Ksv of 0) and an accessible fraction of approximately 60% having a Ka of 4.0 M-1 or 7.0 M-1 for GV-7AW442 or GV-7AW473, respectively.
However, TFIIB did alter the solvent accessibility of GV-7AW473. Its Stern-Volmer plot was downward curved; in a two-species model, approximately 30% of the probe was inaccessible, and the accessible fraction had a Ka of 4.9 M-1.
GV-5HW442 and GV-5HW473 are in-frame fusions of GV to the VP16 activation domain (amino acids 413-490) with the incorporation of 5-hydroxytryptophan at position 442 or 473, respectively.
Protein: DP00087 (UniProt P68336)
Region: residues 413	to 490
Annotation: disorder (Structural state)
Evidence: fluorescence anisotropy evidence used in manual assertion
Supporting statements:
The anisotropy decays of the activator proteins (tested in the absence of target proteins) were best fit to two components: a subnanosecond fast decay component representing segmental motion around the 5-OH-Trp fluorophore and the slower decay component in the range of 2-6 ns. In all of these proteins, the segmental motion contributed at least 60% of the anisotropy decay. The extent of these segmental motions were comparable with those of the known most flexible proteins(42).
The peptides GV-5HW442 and GV-5HW473, studied in this publication, are in-frame fusions of GV to the VP16 activation domain (amino acids 413-490) with the incorporation of 5-hydroxytryptophan at position 442 or 473, respectively.
Protein: DP00087 (UniProt P68336)
Region: residues 413	to 490
Annotation: protein binding (Molecular function)
Evidence: fluorescence anisotropy evidence used in manual assertion
Supporting statements:
The addition of TBP to GV-5HW442 resulted in a large saturable increment in its anisotropy (Fig. 6A), indicating a large decrease in the mobility of the 5-OH-Trp fluorophore. Assuming a 1:1 stoichiometry for the GAL4-VP16•TBP complex, the dissociation constant for the interaction was calculated to be 3.3 (± 1.7) × 10-7M.
When the analog was incorporated at position 473 of the full-length activation domain (GV-5HW473), the anisotropy also increased rapidly as TBP was added to the system, and the anisotropy reached a limiting value (Fig. 6C). The calculated dissociation constant for this interaction is 2.6 (± 0.6) × 10-8M.
GV-5HW442 and GV-5HW473 are in-frame fusions of GV to the VP16 activation domain (amino acids 413-490) with the incorporation of 5-hydroxytryptophan at position 442 or 473, respectively.
Protein: DP00087 (UniProt P68336)
Region: residues 413	to 490
Annotation: molecular function activator activity (Molecular function)
Evidence: fluorescence anisotropy evidence used in manual assertion
Supporting statements:
The addition of TBP to GV-5HW442 resulted in a large saturable increment in its anisotropy (Fig. 6A), indicating a large decrease in the mobility of the 5-OH-Trp fluorophore. Assuming a 1:1 stoichiometry for the GAL4-VP16•TBP complex, the dissociation constant for the interaction was calculated to be 3.3 (± 1.7) × 10-7M.
When the analog was incorporated at position 473 of the full-length activation domain (GV-5HW473), the anisotropy also increased rapidly as TBP was added to the system, and the anisotropy reached a limiting value (Fig. 6C). The calculated dissociation constant for this interaction is 2.6 (± 0.6) × 10-8M.
GV-5HW442 and GV-5HW473 are in-frame fusions of GV to the VP16 activation domain (amino acids 413-490) with the incorporation of 5-hydroxytryptophan at position 442 or 473, respectively.
Protein: DP00087 (UniProt P68336)
Region: residues 413	to 490
Annotation: disorder (Structural state)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
The Trp473 in the full-length activation domain context displayed an emission maximum centered at 349 ± 2 nm, while a C subdomain yielded an emission maximum centered at 348 ± 2 nm. All of these emission wavelength maxima resemble those of fully exposed Trp residues, suggesting that both Trp442 and Trp473 are accessible to solvent.
The fluorescence studies of the VP16 AAD described here showed that this domain was highly flexible and mobile, suggesting that it is poorly structured.
To obtain unique intrinsic fluorescence probes at key positions within the VP16 AAD, Trp mutations were introduced at either position 442 or 473.
Protein: DP00087 (UniProt P68336)
Region: residues 413	to 490
Annotation: disorder (Structural state)
Evidence: fluorescence anisotropy evidence used in manual assertion
Supporting statements:
These small values, in the range of 0.059-0.079, suggest that probes at either position were associated with fast segmental motion as seen in the flexible polypeptide adrenocorticotropin, where rss = 0.06(50).
To obtain unique intrinsic fluorescence probes at key positions within the VP16 AAD, Trp mutations were introduced at either position 442 or 473.
Protein: DP00088 (UniProt P0ABI8)
Region: residues 553	to 663
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Out of the 1,291 residues in cytochrome bo3 ubiquinol oxidase we could assign the sequence for 967 residues (subunit I, 52–81, 96–179, 186–488, 490–520 and 541–552; subunit II, 36–112 and 125–283; subunit III, 19–51, 66–124 and 134–203; subunit IV, 1–109).
Cross-references: PDB:1FFT
Protein: DP00088 (UniProt P0ABI8)
Region: residues 1	to 51
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Out of the 1,291 residues in cytochrome bo3 ubiquinol oxidase we could assign the sequence for 967 residues (subunit I, 52–81, 96–179, 186–488, 490–520 and 541–552; subunit II, 36–112 and 125–283; subunit III, 19–51, 66–124 and 134–203; subunit IV, 1–109).
Cross-references: PDB:1FFT
Protein: DP00089 (UniProt P0ABJ1)
Region: residues 284	to 315
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The 14 N-terminal and 33 C-terminal residues in both CyoA structures are not defined in the electron density (Fig.1).
Cross-references: PDB:1CYW
PDB:1CYX
Protein: DP00089 (UniProt P0ABJ1)
Region: residues 1	to 26
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Out of the 1,291 residues in cytochrome bo3 ubiquinol oxidase we could assign the sequence for 967 residues (subunit I, 52–81, 96–179, 186–488, 490–520 and 541–552; subunit II, 36–112 and 125–283; subunit III, 19–51, 66–124 and 134–203; subunit IV, 1–109).
Cross-references: PDB:1FFT
Protein: DP00089 (UniProt P0ABJ1)
Region: residues 284	to 315
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Out of the 1,291 residues in cytochrome bo3 ubiquinol oxidase we could assign the sequence for 967 residues (subunit I, 52–81, 96–179, 186–488, 490–520 and 541–552; subunit II, 36–112 and 125–283; subunit III, 19–51, 66–124 and 134–203; subunit IV, 1–109).
Cross-references: PDB:1FFT
Protein: DP00090 (UniProt Q14722)
Region: residues 1	to 62
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
 In summary, these results indicated that βN-(1–62) does not exhibit a well defined structure in solution, but rather behaves like a flexible peptide showing only transient formation of local structures.
Protein: DP00090 (UniProt Q14722)
Region: residues 1	to 62
Annotation: flexible N-terminal tail (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
 In summary, these results indicated that βN-(1–62) does not exhibit a well defined structure in solution, but rather behaves like a flexible peptide showing only transient formation of local structures.
Protein: DP00090 (UniProt Q14722)
Region: residues 1	to 62
Annotation: molecular function inhibitor activity (Molecular function)
Evidence: electrophysiology assay evidence used in manual assertion
Supporting statements:
As shown in Fig. 1 B, βN-(1–62) induced rapid inactivation of these channels when present at 50 μm on the cytoplasmic side of the patch; the time-course of inactivation depended on the peptide concentration (not shown).
Protein: DP00090 (UniProt Q14722)
Region: residues 1	to 62
Annotation: protein binding (Molecular function)
Evidence: electrophysiology assay evidence used in manual assertion
Supporting statements:
Wash-off of βN-(1–62), which should reflect unbinding of the peptide from the receptor, exhibited a time constant of ≈100 ms (99.9 ± 16.8 ms, n = 3) and could be well fitted with a monoexponential (Fig. 2 B, right). This indicated that interaction between βN-(1–62) and its receptor on the α-subunit is a first order reaction, with on and off rates (k on, k off) calculated as 1.7 × 106 mol−1 s−1 and 10.3 s−1 (Fig. 2 C).
Protein: DP00091 (UniProt P27088)
Region: residues 1	to 84
Annotation: disorder (Structural state)
Evidence: electrospray ionization fourier transform ion cyclotron resonance mass spectrometry evidence used in manual assertion
Supporting statements:
The highly convoluted spectrum clearly showed there were different charge states of mainly four fragments, all beginning at position Q85 and terminating at R199, R203, K205, and K207.
Thus, we conclude position R84 was more accessible to protease than the uncut sites.
Protein: DP00091 (UniProt P27088)
Region: residues 1	to 84
Annotation: disorder (Structural state)
Evidence: in vitro cleavage assay evidence used in manual assertion
Supporting statements:
Our proteolysis data show long regions of either disorder or flexibility in xXPA, thereby providing an opportunity to evaluate the reliability of PONDR, a neural network predictor originally developed from literature searches of intrinsically ordered and disordered regions in proteins (Romero et al. 1997; Li et al. 1999).
The highly convoluted spectrum clearly showed there were different charge states of mainly four fragments, all beginning at position Q85 and terminating at R199, R203, K205, and K207.
Protein: DP00091 (UniProt P27088)
Region: residues 199	to 265
Annotation: disorder (Structural state)
Evidence: in vitro cleavage assay evidence used in manual assertion
Supporting statements:
Our proteolysis data show long regions of either disorder or flexibility in xXPA, thereby providing an opportunity to evaluate the reliability of PONDR, a neural network predictor originally developed from literature searches of intrinsically ordered and disordered regions in proteins (Romero et al. 1997; Li et al. 1999).
The highly convoluted spectrum clearly showed there were different charge states of mainly four fragments, all beginning at position Q85 and terminating at R199, R203, K205, and K207.
Protein: DP00091 (UniProt P27088)
Region: residues 199	to 265
Annotation: disorder (Structural state)
Evidence: electrospray ionization fourier transform ion cyclotron resonance mass spectrometry evidence used in manual assertion
Supporting statements:
Our proteolysis data show long regions of either disorder or flexibility in xXPA, thereby providing an opportunity to evaluate the reliability of PONDR, a neural network predictor originally developed from literature searches of intrinsically ordered and disordered regions in proteins (Romero et al. 1997; Li et al. 1999).
The highly convoluted spectrum clearly showed there were different charge states of mainly four fragments, all beginning at position Q85 and terminating at R199, R203, K205, and K207.
Protein: DP00092 (UniProt Q08209)
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:
CaNA residues 1-13, 374-468 and 487-521 are not visible in the electron density map.
Cross-references: PDB:1AUI
Protein: DP00092 (UniProt Q08209)
Region: residues 374	to 468
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
CaNA residues 1-13, 374-468 and 487-521 are not visible in the electron density map.
Cross-references: PDB:1AUI
Protein: DP00092 (UniProt Q08209)
Region: residues 487	to 521
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
CaNA residues 1-13, 374-468 and 487-521 are not visible in the electron density map.
Cross-references: PDB:1AUI
Protein: DP00092 (UniProt Q08209)
Region: residues 373	to 466
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
To analyze the secondary structure of the RD, we obtained CD spectra of the RD alone. The spectrum is consistent with that of an unstructured polypeptide chain (Figure 4a).
Protein: DP00092 (UniProt Q08209)
Region: residues 373	to 466
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
To analyze the secondary structure of the RD, we obtained CD spectra of the RD alone. The spectrum is consistent with that of an unstructured polypeptide chain (Figure 4a).
However, an equimolar mixture of CaM and the RD demonstrates that the RD:CaM complex has greater helical content than the pCaN:CaM complex (Figure 4a).
Protein: DP00092 (UniProt Q08209)
Region: residues 373	to 466
Annotation: calmodulin binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
However, an equimolar mixture of CaM and the RD demonstrates that the RD:CaM complex has greater helical content than the pCaN:CaM complex (Figure 4a).
Protein: DP00092 (UniProt Q08209)
Region: residues 373	to 468
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Authors show that when in complex with calmodulin, this region of the protein has greater helical content.
Protein: DP00092 (UniProt Q08209)
Region: residues 373	to 468
Annotation: calmodulin binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Authors show that when in presence of calmodulin the CD spectra changes, indicating the formation of a complex.
Protein: DP00092 (UniProt Q08209)
Region: residues 1	to 13
Annotation: flexible N-terminal tail (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
CaNA residues 1-13, 374-468 and 487-521 are not visible in the electron density map.
Cross-references: PDB:1AUI
Protein: DP00092 (UniProt Q08209)
Region: residues 487	to 521
Annotation: flexible C-terminal tail (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
CaNA residues 1-13, 374-468 and 487-521 are not visible in the electron density map.
Cross-references: PDB:1AUI
Protein: DP00092 (UniProt Q08209)
Region: residues 373	to 466
Annotation: order (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
However, an equimolar mixture of CaM and the RD demonstrates that the RD:CaM complex has greater helical content than the pCaN:CaM complex (Figure 4a).
Protein: DP00092 (UniProt Q08209)
Region: residues 388	to 466
Annotation: calmodulin binding (Molecular function)
Evidence: fluorescence resonance energy transfer evidence used in manual assertion
Supporting statements:
Ensemble average distances (rFRET) for this FRET pair in the RDc bound to CaM at 20 and 50 °C are shown in Figure 5a.
CaM Binding Brings the Termini of the RD Together