SMTL ID : 4ibv.1

Human p53 core domain with hot spot mutation R273C and second-site suppressor mutation S240R in sequence-specific complex with DNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: H.85, R.88, C.89 Chain C: P.84, G.151 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:G.151, A:H.85, A:H.85, A:C.89 EDO.2: 6 residues within 4Å: Chain A: S.73, Q.74, H.75, M.76, T.77, E.78 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.73, A:T.77 Water bridges: A:Q.74, A:E.78 EDO.3: 4 residues within 4Å: Chain A: P.59, D.166, S.167, S.168 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.167, A:S.167, A:S.168 Water bridges: A:T.62 EDO.4: 6 residues within 4Å: Chain A: G.61, T.62, R.63, P.126, Y.127 Ligands: EDO.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.61, A:Y.127 EDO.5: 2 residues within 4Å: Chain A: K.8, T.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.8 Water bridges: A:T.9, A:T.9 EDO.6: 9 residues within 4Å: Chain A: T.57, P.58, P.59, P.60, G.61, T.62, Y.127, P.129 Ligands: EDO.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.61, A:T.62, A:T.62 EDO.7: 4 residues within 4Å: Chain A: E.87, R.88, S.90, P.98 No protein-ligand interaction detected (PLIP) EDO.9: 5 residues within 4Å: Chain A: P.84, G.151 Chain C: H.85, R.88, C.89 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:G.151, C:H.85, C:C.89 EDO.10: 6 residues within 4Å: Chain C: S.73, Q.74, H.75, M.76, T.77, E.78 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.73, C:T.77 Water bridges: C:Q.74, C:E.78 EDO.11: 4 residues within 4Å: Chain C: P.59, D.166, S.167, S.168 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.166, C:S.167, C:S.167, C:S.168 EDO.12: 6 residues within 4Å: Chain C: G.61, T.62, R.63, P.126, Y.127 Ligands: EDO.14 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.61, C:Y.127 EDO.13: 2 residues within 4Å: Chain C: K.8, T.9 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.8 Water bridges: C:T.9, C:T.9 EDO.14: 9 residues within 4Å: Chain C: T.57, P.58, P.59, P.60, G.61, T.62, Y.127, P.129 Ligands: EDO.12 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.61, C:T.62, C:T.62 EDO.15: 4 residues within 4Å: Chain C: E.87, R.88, S.90, P.98 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.8: 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.16: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Eldar, A. et al., Structural studies of p53 inactivation by DNA-contact mutations and its rescue by suppressor mutations via alternative protein-DNA interactions. Nucleic Acids Res. (2013)

Release Date

2013-08-14

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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