SMTL ID : 5mcu.1

New Insights into the Role of DNA Shape on Its Recognition by p53 Proteins (complex p53DBD-LHG2)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 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.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.9: 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.13: 4 residues within 4Å: Chain E: C.83, H.86, C.145, 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: 8 residues within 4Å: Chain A: K.39, S.147, 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:S.147 EDO.3: 7 residues within 4Å: Chain A: F.20, L.21, C.31, T.32, Y.33, M.40, P.49 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.21, A:C.31, A:P.49 Water bridges: A:S.23 EDO.4: 4 residues within 4Å: Chain A: D.114, D.115, R.116, F.119 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.114 EDO.6: 8 residues within 4Å: Chain B: K.39, S.147, 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:S.147 EDO.7: 6 residues within 4Å: Chain B: F.20, L.21, C.31, Y.33, M.40, P.49 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.21, B:C.31, B:P.49 Water bridges: B:S.23 EDO.8: 4 residues within 4Å: Chain B: D.114, D.115, R.116, F.119 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.114 EDO.10: 8 residues within 4Å: Chain D: K.39, S.147, P.157, I.158, E.178, V.179, R.180, E.192 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:K.39, D:V.179, D:R.180 Water bridges: D:S.147 EDO.11: 7 residues within 4Å: Chain D: F.20, L.21, C.31, T.32, Y.33, M.40, P.49 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:L.21, D:C.31, D:P.49 Water bridges: D:S.23 EDO.12: 4 residues within 4Å: Chain D: D.114, D.115, R.116, F.119 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.114 EDO.14: 8 residues within 4Å: Chain E: K.39, S.147, P.157, I.158, E.178, V.179, R.180, E.192 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:K.39, E:V.179, E:R.180 Water bridges: E:S.147 EDO.15: 6 residues within 4Å: Chain E: F.20, L.21, C.31, Y.33, M.40, P.49 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:L.21, E:C.31, E:P.49 Water bridges: E:S.23 EDO.16: 4 residues within 4Å: Chain E: D.114, D.115, R.116, F.119 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.114

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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