SMTL ID : 7b4g.1

Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ). Human p53DBD-R282W mutant bound to DNA: R282W-MQ (II)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.83, H.86, C.145, C.149 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.83, A:H.86, A:C.145, A:C.149 ZN.7: 4 residues within 4Å: Chain C: C.83, H.86, C.145, C.149 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.83, C:H.86, C:C.145, C:C.149

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 4 residues within 4Å: Chain A: R.187, D.188, T.191 Chain D: T.7 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.191 EDO.3: 2 residues within 4Å: Chain A: E.131, V.132 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.132 EDO.5: 5 residues within 4Å: Chain A: F.20, L.21, H.22, Y.33, P.35 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.21 EDO.6: 3 residues within 4Å: Chain A: E.105, G.106, H.140 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.140 Water bridges: A:N.107, A:H.140 EDO.8: 4 residues within 4Å: Chain B: T.7 Chain C: R.187, D.188, T.191 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.188, C:T.191 Water bridges: C:T.191 EDO.9: 2 residues within 4Å: Chain C: E.131, V.132 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.131, C:V.132 EDO.11: 5 residues within 4Å: Chain C: F.20, L.21, H.22, Y.33, P.35 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:L.21 EDO.12: 3 residues within 4Å: Chain C: E.105, G.106, H.140 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.140 Water bridges: C:N.107, C:H.140

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 5 residues within 4Å: Chain A: K.27, R.187, R.190 Chain B: G.2, G.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.190 Water bridges: A:K.27 PEG.10: 5 residues within 4Å: Chain C: K.27, R.187, R.190 Chain D: G.2, G.3 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.190 Water bridges: C:K.27

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Degtjarik, O. et al., Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ). Nat Commun (2021)

Release Date

2021-12-08

Peptides

Cellular tumor antigen p53: AC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

Cellular tumor antigen p53

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