SMTL ID : 8dc6.1 (3 other biounits)

Crystal structure of p53 Y220C covalently bound to indole KG6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.87, H.90, C.149, C.153 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.87, A:H.90, A:C.149, A:C.153

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: Q.76, Q.78, H.79 Ligands: SO4.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.76, A:Q.78 Salt bridges: A:H.79 SO4.3: 4 residues within 4Å: Chain A: T.13, Y.14, Q.15, G.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.15, A:G.16 SO4.4: 5 residues within 4Å: Chain A: R.86, S.94, D.95, R.107, M.148 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.94, A:D.95, A:D.95 Salt bridges: A:R.86, A:R.107 SO4.5: 2 residues within 4Å: Chain A: R.159, R.184 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.159, A:R.184 Salt bridges: A:R.184 SO4.6: 3 residues within 4Å: Chain A: Q.76, Q.78 Ligands: SO4.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.76, A:Q.78

1 x R4F: 1-(2-methylprop-2-enoyl)-1H-indole-3-carbaldehyde, bound form(Covalent)

R4F.7: 12 residues within 4Å: Chain A: L.56, V.58, V.68, V.129, P.130, C.131, E.132, P.134, S.138, D.139, S.140, T.141 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.56, A:V.58, A:V.58, A:V.68, A:V.129, A:T.141

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guiley, K.Z. et al., A Small Molecule Reacts with the p53 Somatic Mutant Y220C to Rescue Wild-type Thermal Stability. Cancer Discov (2023)

Release Date

2022-10-12

Peptides

Cellular tumor antigen p53: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cellular tumor antigen p53

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