SMTL ID : 7b46.1

Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ). Human wild-type p53DBD bound to DNA and MQ: wt-DNA-MQ (P1)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

homo-tetramer

Ligands

4 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.5: 4 residues within 4Å: Chain B: C.83, H.86, C.145, C.149 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.83, B:H.86, B:C.145, B:C.149 ZN.8: 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 ZN.11: 4 residues within 4Å: Chain D: C.83, H.86, C.145, C.149 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.83, D:H.86, D:C.145, D:C.149

7 x QN8: (2~{R})-2-methyl-1-azabicyclo[2.2.2]octan-3-one(Covalent)

QN8.2: 3 residues within 4Å: Chain A: K.8, Y.10, L.171 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.8, A:Y.10, A:Y.10, A:L.171 QN8.3: 5 residues within 4Å: Chain A: Q.51, W.53, S.134, D.135, C.136 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.53 Hydrogen bonds: A:S.134, A:D.135 QN8.4: 9 residues within 4Å: Chain A: K.27, S.28, Q.43, A.183, C.184 Chain E: G.2, G.3 Chain F: C.9, C.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.43 QN8.6: 8 residues within 4Å: Chain B: K.27, Q.43, A.183, C.184 Chain E: C.9, C.10 Chain F: G.2, G.3 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.43 QN8.9: 4 residues within 4Å: Chain C: Q.51, S.134, D.135, C.136 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.135 QN8.10: 10 residues within 4Å: Chain C: K.27, S.28, Q.43, A.183, C.184 Chain G: C.9, C.10 Chain H: C.1, G.2, G.3 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:K.27 Hydrogen bonds: C:Q.43 QN8.13: 9 residues within 4Å: Chain D: K.27, S.28, Q.43, A.183, C.184 Chain G: G.2, G.3 Chain H: C.9, C.10 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.43

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 4 residues within 4Å: Chain B: K.71, Q.72, S.73 Chain C: G.106 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.73 Water bridges: B:S.73, B:S.73, B:Q.74

1 x QNN: (2~{S})-2-methyl-1-azabicyclo[2.2.2]octan-3-one(Covalent)

QNN.12: 4 residues within 4Å: Chain D: Q.51, S.134, D.135, C.136 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.135

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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Cellular tumor antigen p53

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