LiteFold/DisProt huggingface dataset:
Protein: DP00086 (UniProt P04637)
Region: residues 37	to 57
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Here we report the crystal structure of RPA residues 1-120 (RPA70N) bound to the N-terminal transactivation domain of p53 (residues 37-57; p53N) and, by using NMR spectroscopy, characterize two mechanisms by which the RPA/p53 interaction can be modulated.
In contrast, the N-terminal p53 transactivation domain is largely disordered in solution, but residues 37-57 fold into two amphipathic helices, H1 and H2, upon binding with RPA70N.
Cross-references: PDB:2B3G
Protein: DP00086 (UniProt P04637)
Region: residues 17	to 29
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The crystal structure of the 109-residue amino-terminal domain of MDM2 bound to a 15-residue transactivation domain peptide of p53 revealed that MDM2 has a deep hydrophobic cleft on which the p53 peptide binds as an amphipathic alpha helix.
Cross-references: PDB:1YCR
Protein: DP00086 (UniProt P04637)
Region: residues 15	to 29
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The crystal structure of the 109-residue amino-terminal domain of MDM2 bound to a 15-residue transactivation domain peptide of p53 revealed that MDM2 has a deep hydrophobic cleft on which the p53 peptide binds as an amphipathic alpha helix.
Cross-references: PDB:1YCR
Protein: DP00086 (UniProt P04637)
Region: residues 367	to 386
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Here, we report that the conserved bromo-domain of the transcriptional coactivator CBP (CREB binding protein) binds specifically to p53 at the C-terminal acetylated lysine 382. This bromodomain/acetyl-lysine binding is responsible for p53 acetylation-dependent coactivator recruitment after DNA damage, a step essential for p53-induced transcriptional activation of the cyclin-dependent kinase inhibitor p21 in G1 cell cycle arrest.
Cross-references: PDB:1JSP
Protein: DP00086 (UniProt P04637)
Region: residues 367	to 386
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
This binding is dependent upon K382 acetylation of the peptide with a KD of ∼50 μM, as estimated from NMR titration.
These results confirm that the CBP bromodomain can specifically interact with p53 acetylated at K382.
Cross-references: PDB:1JSP
Protein: DP00086 (UniProt P04637)
Region: residues 380	to 384
Annotation: acetylation display site (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
This binding is dependent upon K382 acetylation of the peptide with a KD of ∼50 μM, as estimated from NMR titration.
Cross-references: PDB:1JSP
Protein: DP00086 (UniProt P04637)
Region: residues 367	to 386
Annotation: molecular function activator activity (Molecular function)
Evidence: enzyme-linked immunoabsorbent assay evidence used in manual assertion
Supporting statements:
p53-Induced p21 Activation Requires the CBP Bromodomain/p53 AcK382 Interaction
Cross-references: PDB:1JSP
Protein: DP00086 (UniProt P04637)
Region: residues 367	to 386
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
P53 region 367-386 binds to CBP upon K382 acetylation and undergoes disorder-to-order transition upon binding
Cross-references: PDB:1JSP
Protein: DP00086 (UniProt P04637)
Region: residues 47	to 58
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Here, we reveal the recognition mechanism of the phosphorylated TAD2 bound to a pleckstrin homology (PH) domain from human TFIIH subunit p62 in an extended string-like conformation.
Although the isolated phosphorylated TAD2 seems to be intrinsically disordered, an extended and ordered structure was induced between residues 47–58 upon binding to the PH domain 
Cross-references: PDB:2RUK
Protein: DP00086 (UniProt P04637)
Region: residues 41	to 62
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Here, we reveal the recognition mechanism of the phosphorylated TAD2 bound to a pleckstrin homology (PH) domain from human TFIIH subunit p62 in an extended string-like conformation.
Cross-references: PDB:2RUK
Protein: DP00086 (UniProt P04637)
Region: residues 15	to 29
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
 We have determined the crystal structure of the N-terminal domain of human Mdmx bound to a 15-residue transactivation domain peptide of human p53.
Cross-references: PDB:3DAB
Protein: DP00086 (UniProt P04637)
Region: residues 17	to 27
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
 We have determined the crystal structure of the N-terminal domain of human Mdmx bound to a 15-residue transactivation domain peptide of human p53.
The surface area occupied by aminoacids 17–27 of the p53 peptide has 440 Å2 for human Mdmx and 407 Å2 for zebrafish Mdmx.
Cross-references: PDB:3DAB
PDB:3DAC
Protein: DP00086 (UniProt P04637)
Region: residues 1	to 93
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The A box interacts with residues 38-61 (TAD2) of the p53 transactivation domain. Residues 19-26 (TAD1) bind weakly, but only in the context of p53(1-93) and not as a free TAD1 peptide. We have solved the structure of the A-box/p53(1-93) complex by nuclear magnetic resonance spectroscopy.
Cross-references: PDB:2LY4
Protein: DP00086 (UniProt P04637)
Region: residues 1	to 93
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Residues with resonances undergoing significant chemical-shift changes were located in the region spanning residues 18–57, which contains the elements of nascent secondary structure, namely TAD1 (residues 14–28) and TAD2 (residues 38–61) (Lee et al., 2000), with the largest changes occurring in TAD2.
Protein: DP00086 (UniProt P04637)
Region: residues 1	to 93
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
The isolated p53(1–93) fragment and the A box interact (Figure 2F), and an estimate of the affinity (Kd 346 nM) was obtained by isothermal titration calorimetry (ITC)
Protein: DP00086 (UniProt P04637)
Region: residues 14	to 60
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Residues with resonances undergoing significant chemical-shift changes were located in the region spanning residues 18–57, which contains the elements of nascent secondary structure, namely TAD1 (residues 14–28) and TAD2 (residues 38–61) (Lee et al., 2000), with the largest changes occurring in TAD2.
Protein: DP00086 (UniProt P04637)
Region: residues 369	to 377
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The crystal structure of a ternary complex of Set9 with a p53 peptide and the cofactor product S-adenosyl-l-homocysteine (AdoHcy) provides the molecular basis for recognition of p53 by this lysine methyltransferase.
Cross-references: PDB:1XQH
Protein: DP00086 (UniProt P04637)
Region: residues 359	to 367
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
We show that the N-terminal domain of USP7 binds two closely spaced 4-residue sites in both p53 and MDM2, falling between p53 residues 359-367 and MDM2 residues 147-159.
Cross-references: PDB:2FOO
PDB:2FOJ
Protein: DP00086 (UniProt P04637)
Region: residues 366	to 386
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Here we detail the molecular mechanisms for the recognition of p53K370me2 and p53K382me2 by 53BP1. The solution structures of TTD in complex with the p53K370me2 and p53K382me2 peptides show a remarkable plasticity of 53BP1 in accommodating these diverse dimethyllysine-containing sequences. We demonstrate that dimeric TTDs are capable of interacting with the two PTMs on a single p53K370me2K382me2 peptide, greatly strengthening the 53BP1-p53 interaction.
Cross-references: PDB:2MWP
PDB:2MWO
Protein: DP00086 (UniProt P04637)
Region: residues 366	to 386
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Here we detail the molecular mechanisms for the recognition of p53K370me2 and p53K382me2 by 53BP1. The solution structures of TTD in complex with the p53K370me2 and p53K382me2 peptides show a remarkable plasticity of 53BP1 in accommodating these diverse dimethyllysine-containing sequences. We demonstrate that dimeric TTDs are capable of interacting with the two PTMs on a single p53K370me2K382me2 peptide, greatly strengthening the 53BP1-p53 interaction.
Cross-references: PDB:2MWP
PDB:2MWO
Protein: DP00086 (UniProt P04637)
Region: residues 366	to 386
Annotation: protein binding (Molecular function)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
Here we detail the molecular mechanisms for the recognition of p53K370me2 and p53K382me2 by 53BP1. The solution structures of TTD in complex with the p53K370me2 and p53K382me2 peptides show a remarkable plasticity of 53BP1 in accommodating these diverse dimethyllysine-containing sequences. We demonstrate that dimeric TTDs are capable of interacting with the two PTMs on a single p53K370me2K382me2 peptide, greatly strengthening the 53BP1-p53 interaction.
Protein: DP00086 (UniProt P04637)
Region: residues 385	to 393
Annotation: 14-3-3 protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Here, we report the crystal structure of the extreme C-terminus (residues 385-393, p53pT387) of p53 in complex with 14-3-3sigma at a resolution of 1.28A.
Cross-references: PDB:3LW1
Protein: DP00086 (UniProt P04637)
Region: residues 372	to 389
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Crystal structure of Sir2, residues 1-246, bound to the C-terminal domain of p53, residues 372-389.
Cross-references: PDB:2H4J
Protein: DP00086 (UniProt P04637)
Region: residues 375	to 385
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Crystal structure of Sir2, residues 1-246, bound to the C-terminal domain of p53, residues 372-389.
Cross-references: PDB:2H4J
Protein: DP00086 (UniProt P04637)
Region: residues 367	to 388
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
A peptide derived from this region of p53 (residues 367-388) was found to have no regular structure in its native form by NMR spectroscopy, but becomes helical when bound to Ca2+ loaded S100B(betabeta).
Cross-references: PDB:1DT7
Protein: DP00086 (UniProt P04637)
Region: residues 367	to 388
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
A peptide derived from this region of p53 (residues 367-388) was found to have no regular structure in its native form by NMR spectroscopy, but becomes helical when bound to Ca2+ loaded S100B(betabeta).
Cross-references: PDB:1DT7
Protein: DP00086 (UniProt P04637)
Region: residues 376	to 386
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Crystal structure of a C-terminal 11-residue recruitment peptide of P53 in complex with CDK2/CyclinA
Cross-references: PDB:1H26
Protein: DP00086 (UniProt P04637)
Region: residues 372	to 389
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Crystal structure of a C-terminal acetylated (Lys382) peptide of P53 bound to Sir2 homologue from Thermatoga maritima (Sir2Tm). 
Cross-references: PDB:2H2D
Protein: DP00086 (UniProt P04637)
Region: residues 365	to 375
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
We have solved the high resolution crystal structures of the full-length SMYD2 protein in binary complex with its cofactor S-adenosylmethionine and in ternary complex with cofactor product S-adenosylhomocysteine and p53 substrate peptide (residues 368-375), respectively.
Cross-references: PDB:3TG5
Protein: DP00086 (UniProt P04637)
Region: residues 368	to 372
Annotation: methylation display site (Disorder function)
Evidence: methylation assay evidence used in manual assertion
Supporting statements:
SMYD2 belongs to a subfamily of histone lysine methyltransferase and was recently identified to methylate tumor suppressor p53 and Rb. Here we report that SMYD2 prefers to methylate p53 Lys-370 over histone substrates in vitro. Consistently, the level of endogenous p53 Lys-370 monomethylation is significantly elevated when SMYD2 is overexpressed in vivo.
CTD Domain and EDEE Motif Are Important for p53 Lys-370 Methylation by SMYD2
Cross-references: PDB:3TG5
Protein: DP00086 (UniProt P04637)
Region: residues 379	to 385
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Crystal structure of a C-terminal peptide of P53 in complex with Sirt1
Cross-references: PDB:4ZZJ
Protein: DP00086 (UniProt P04637)
Region: residues 1	to 39
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Here, we report the NMR structure of the complex of the Taz2 (C/H3) domain of p300 and the N-terminal transactivation domain of p53. In the complex, p53 forms a short alpha helix and interacts with the Taz2 domain through an extended surface.
Cross-references: PDB:2K8F
Protein: DP00086 (UniProt P04637)
Region: residues 1	to 39
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Here, we report the NMR structure of the complex of the Taz2 (C/H3) domain of p300 and the N-terminal transactivation domain of p53. In the complex, p53 forms a short alpha helix and interacts with the Taz2 domain through an extended surface.
Cross-references: PDB:2K8F
Protein: DP00086 (UniProt P04637)
Region: residues 14	to 19
Annotation: phosphorylation display site (Disorder function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
Our structural and binding studies allow better understanding of the molecular basis for the increased binding affinity between Taz2 and p531-39 upon phosphorylation at Ser15 and Thr18.
Cross-references: PDB:2K8F
Protein: DP00086 (UniProt P04637)
Region: residues 42	to 56
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Figure 5a shows that residues 39–59 have the largest resonance intensity changes in the presence of hRPA701–168 with residues 42–56 having intensity ratios that are >10.
Protein: DP00086 (UniProt P04637)
Region: residues 42	to 56
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The amide 1H and 15N chemical shifts of an uniformly 15N-labeled sample of p53TAD were also monitored before and after the addition of unlabeled hRPA701-168. In the presence of unlabeled hRPA701-168, resonance lineshapes increased and corresponding intensity reductions were observed for specific p53TAD residues. The largest intensity reductions were observed for p53TAD residues 42-56.
Protein: DP00086 (UniProt P04637)
Region: residues 1	to 73
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
For instance, the mean values of R1, R2, R1ρ and the NHNOE for free p53TAD are consistent with values expected for an intrinsically unstructured protein (67).
Protein: DP00086 (UniProt P04637)
Region: residues 1	to 73
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectrum of p53 TAD peptide at neutral pH showed no apparent alpha-helical structure when analyzed byYang’s method (Fig. 4A; Ref. 50).
Although the text only mentions the lack of a helical structure, the CD spectrum shows that the peptide is in fact disordered.
Protein: DP00086 (UniProt P04637)
Region: residues 1	to 73
Annotation: molecular function activator activity (Molecular function)
Evidence: bait-prey hybrid interaction evidence used in manual assertion
Supporting statements:
The p53 TAD and mutant derivatives were assayed for the ability to bind in vitro translated human TBP in a GST pull-down assay as described under“Materials and Methods.”
As shown in Fig.3Band Table I, the levels of TBP precipitated by GST-p53 TAD and mutant derivatives are linearly correlated with the abilityof transactivation in vivo.
Protein: DP00086 (UniProt P04637)
Region: residues 1	to 73
Annotation: protein binding (Molecular function)
Evidence: bait-prey hybrid interaction evidence used in manual assertion
Supporting statements:
As shown in Fig.3Band Table I, the levels of TBP precipitated by GST-p53 TAD and mutant derivatives are linearly correlated with the abilityof transactivation in vivo.
Protein: DP00086 (UniProt P04637)
Region: residues 20	to 46
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The p53 TAD2 in the complex is unstructured except for a short amphipathic α helix involving residues 47–55.
Chemical shift analysis and the NOE pattern demonstrated that p53 in complex with Tfb1 adopts an a-helical fold that extends from Pro47 to Thr55. Outside this region, p53 is flexible, as also supported by the 15N-1H heteronuclear NOE data.
Cross-references: PDB:2GS0
Protein: DP00086 (UniProt P04637)
Region: residues 56	to 70
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The p53 TAD2 in the complex is unstructured except for a short amphipathic α helix involving residues 47–55.
Chemical shift analysis and the NOE pattern demonstrated that p53 in complex with Tfb1 adopts an a-helical fold that extends from Pro47 to Thr55. Outside this region, p53 is flexible, as also supported by the 15N-1H heteronuclear NOE data.
Cross-references: PDB:2GS0
Protein: DP00086 (UniProt P04637)
Region: residues 1	to 61
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The N-terminal region is dynamically disordered in the full-length p53 tetramer, fluctuating between states in which it is free and fully exposed to solvent and states in which it makes transient contacts with the DNA-binding domain (DBD).
The cross-peaks in the spectrum of uniformly labeled p53 (black in Fig. 1C) are from residues in the disordered regions: The resonances of the folded DBD and TET domains are severely broadened in HSQC spectra of the 180-kDa tetramer, and their resonances are not visible.
Protein: DP00086 (UniProt P04637)
Region: residues 1	to 61
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The N-terminal region is dynamically disordered in the full-length p53 tetramer, fluctuating between states in which it is free and fully exposed to solvent and states in which it makes transient contacts with the DNA-binding domain (DBD).
In addition to the chemical shift changes, residues in both AD1 and AD2 have decreased cross-peak intensity in the p53 tetramer relative to the peptide (Fig. 2C). While the intensity loss is greater for AD2 than AD1, it is clear that intramolecular interactions within full-length p53 affect the conformational ensemble and dynamics of both motifs.
Cross-peaks in spectra of 15N-labeled p53(1–61), p53(1–312), and 15NNTAD–p53 fall along a line, suggesting that p53(1–312) and the segmentally labeled full-length p53 experience the same two-site exchange process between states in which the NTAD is free or bound to the DBD.
Protein: DP00086 (UniProt P04637)
Region: residues 14	to 28
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
With the spin label at S15C, cross-peaks of residues in both the AD1 and AD2 regions are broadened; similarly, attachment of the spin label at P58C broadens resonances associated with both the AD2 and AD1 motifs, confirming the presence of interactions between these motifs (SI Appendix, Fig. S4). Transient interactions between the AD1 and AD2 regions have been observed previously in isolated NTAD peptides (59). In addition, selective resonance broadening is observed for several DBD cross-peaks (SI Appendix, Fig. S4), indicating intramolecular interactions between the spin labeled NTAD and the DBD.
With the spin label at P58C (AD2), the largest PRE is observed for residues located in the DNA-binding site; these include T118 and V122 in the L1 loop, G245 and to a lesser extent N247 in the L3 loop, A276, and G279, R280, and R283 in the C-terminal helix.
Protein: DP00086 (UniProt P04637)
Region: residues 38	to 61
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
With the spin label at S15C, cross-peaks of residues in both the AD1 and AD2 regions are broadened; similarly, attachment of the spin label at P58C broadens resonances associated with both the AD2 and AD1 motifs, confirming the presence of interactions between these motifs (SI Appendix, Fig. S4). Transient interactions between the AD1 and AD2 regions have been observed previously in isolated NTAD peptides (59). In addition, selective resonance broadening is observed for several DBD cross-peaks (SI Appendix, Fig. S4), indicating intramolecular interactions between the spin labeled NTAD and the DBD.
With the spin label at P58C (AD2), the largest PRE is observed for residues located in the DNA-binding site; these include T118 and V122 in the L1 loop, G245 and to a lesser extent N247 in the L3 loop, A276, and G279, R280, and R283 in the C-terminal helix.
Protein: DP00086 (UniProt P04637)
Region: residues 1	to 61
Annotation: self-inhibition (Disorder function)
Evidence: fluorescence anisotropy 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.