SMTL ID : 5mct.1

New Insights into the Role of DNA Shape on Its Recognition by p53 Proteins (complex p53DBD-LHG1)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.83, H.86, C.145, N.146, 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.6: 5 residues within 4Å: Chain B: C.83, H.86, C.145, N.146, 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.11: 5 residues within 4Å: Chain D: C.83, H.86, C.145, N.146, C.149 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.83, D:H.86, D:C.145, D:C.149 ZN.16: 5 residues within 4Å: Chain E: C.83, H.86, C.145, N.146, C.149 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.83, E:H.86, E:C.145, E:C.149

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

EDO.2: 9 residues within 4Å: Chain A: K.39, S.147, R.155, P.157, I.158, E.178, V.179, R.180, E.192 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.39, A:V.179, A:R.180 Water bridges: A:E.192 EDO.3: 4 residues within 4Å: Chain A: R.17, L.18, G.19, W.53 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.17, A:L.18 Water bridges: A:F.20 EDO.4: 7 residues within 4Å: Chain A: F.20, L.21, S.23, C.31, T.32, Y.33, P.49 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.21, A:S.23, A:S.23, A:P.49 Water bridges: A:S.23 EDO.7: 9 residues within 4Å: Chain B: K.39, S.147, R.155, P.157, I.158, E.178, V.179, R.180, E.192 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.39, B:V.179, B:R.180 Water bridges: B:E.192 EDO.8: 7 residues within 4Å: Chain B: F.20, L.21, S.23, C.31, T.32, Y.33, P.49 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.21, B:S.23, B:S.23, B:P.49 Water bridges: B:S.23 EDO.9: 4 residues within 4Å: Chain B: R.17, L.18, G.19, W.53 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.17, B:L.18 Water bridges: B:F.20 EDO.12: 9 residues within 4Å: Chain D: K.39, S.147, R.155, P.157, I.158, E.178, V.179, R.180, E.192 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:K.39, D:E.178, D:V.179, D:R.180 Water bridges: D:E.192 EDO.13: 4 residues within 4Å: Chain D: R.17, L.18, G.19, W.53 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.17, D:L.18 Water bridges: D:F.20 EDO.14: 7 residues within 4Å: Chain D: F.20, L.21, S.23, C.31, T.32, Y.33, P.49 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:L.21, D:S.23, D:S.23, D:P.49 Water bridges: D:S.23 EDO.17: 9 residues within 4Å: Chain E: K.39, S.147, R.155, P.157, I.158, E.178, V.179, R.180, E.192 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:K.39, E:E.178, E:V.179, E:R.180 Water bridges: E:E.192 EDO.18: 7 residues within 4Å: Chain E: F.20, L.21, S.23, C.31, T.32, Y.33, P.49 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:L.21, E:S.23, E:S.23, E:P.49 Water bridges: E:S.23 EDO.19: 4 residues within 4Å: Chain E: R.17, L.18, G.19, W.53 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.17, E:L.18 Water bridges: E:F.20

4 x FOR: FORMYL GROUP(Non-covalent)

FOR.5: 3 residues within 4Å: Chain A: N.38, L.159, E.178 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.178 FOR.10: 5 residues within 4Å: Chain B: N.38, K.71, L.159, F.177, E.178 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.178 FOR.15: 3 residues within 4Å: Chain D: N.38, L.159, E.178 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.178 FOR.20: 5 residues within 4Å: Chain E: N.38, K.71, L.159, F.177, E.178 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.178

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Golovenko, D. et al., New Insights into the Role of DNA Shape on Its Recognition by p53 Proteins. Structure (2018)

Release Date

2018-06-13

Peptides

Cellular tumor antigen p53: ABDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
A

E
B

Cellular tumor antigen p53

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