SMTL ID : 5mcv.1

New Insights into the Role of DNA Shape on Its Recognition by p53 Proteins (complex p53DBD-LWC1)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: C.83, H.86, C.145, N.146, C.149 Chain E: M.150 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.83, A:H.86, A:C.145, A:C.149 ZN.8: 6 residues within 4Å: Chain B: C.83, H.86, C.145, N.146, C.149 Chain D: M.150 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.83, B:H.86, B:C.145, B:C.149 ZN.15: 6 residues within 4Å: Chain B: M.150 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.22: 6 residues within 4Å: Chain A: M.150 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

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

EDO.2: 7 residues within 4Å: Chain A: F.20, L.21, S.23, C.31, T.32, Y.33, P.49 Ligand excluded by PLIP EDO.3: 8 residues within 4Å: Chain A: K.39, S.147, P.157, I.158, E.178, V.179, R.180, E.192 Ligand excluded by PLIP EDO.4: 2 residues within 4Å: Chain A: S.167, S.168 Ligand excluded by PLIP EDO.5: 7 residues within 4Å: Chain A: Q.7, L.37, N.38, K.71, L.159, F.177, E.178 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: R.17, L.18, G.19, W.53 Ligands: ACT.7 Ligand excluded by PLIP EDO.9: 7 residues within 4Å: Chain B: F.20, L.21, S.23, C.31, T.32, Y.33, P.49 Ligand excluded by PLIP EDO.10: 8 residues within 4Å: Chain B: K.39, S.147, P.157, I.158, E.178, V.179, R.180, E.192 Ligand excluded by PLIP EDO.11: 2 residues within 4Å: Chain B: S.167, S.168 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain B: R.17, L.18, G.19, W.53 Ligands: ACT.14 Ligand excluded by PLIP EDO.13: 7 residues within 4Å: Chain B: Q.7, L.37, N.38, K.71, L.159, F.177, E.178 Ligand excluded by PLIP EDO.16: 7 residues within 4Å: Chain D: F.20, L.21, S.23, C.31, T.32, Y.33, P.49 Ligand excluded by PLIP EDO.17: 8 residues within 4Å: Chain D: K.39, S.147, P.157, I.158, E.178, V.179, R.180, E.192 Ligand excluded by PLIP EDO.18: 2 residues within 4Å: Chain D: S.167, S.168 Ligand excluded by PLIP EDO.19: 7 residues within 4Å: Chain D: Q.7, L.37, N.38, K.71, L.159, F.177, E.178 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain D: R.17, L.18, G.19, W.53 Ligands: ACT.21 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain E: F.20, L.21, S.23, C.31, T.32, Y.33, P.49 Ligand excluded by PLIP EDO.24: 8 residues within 4Å: Chain E: K.39, S.147, P.157, I.158, E.178, V.179, R.180, E.192 Ligand excluded by PLIP EDO.25: 2 residues within 4Å: Chain E: S.167, S.168 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain E: R.17, L.18, G.19, W.53 Ligands: ACT.28 Ligand excluded by PLIP EDO.27: 7 residues within 4Å: Chain E: Q.7, L.37, N.38, K.71, L.159, F.177, E.178 Ligand excluded by PLIP

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

ACT.7: 5 residues within 4Å: Chain A: L.18, G.19, F.20, Y.33 Ligands: EDO.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.20, A:Y.33 Hydrogen bonds: A:Y.33 Water bridges: A:L.18, A:L.18, A:Y.33 ACT.14: 5 residues within 4Å: Chain B: L.18, G.19, F.20, Y.33 Ligands: EDO.12 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.20, B:Y.33 Hydrogen bonds: B:Y.33 Water bridges: B:L.18, B:L.18, B:Y.33 ACT.21: 5 residues within 4Å: Chain D: L.18, G.19, F.20, Y.33 Ligands: EDO.20 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:F.20, D:Y.33 Hydrogen bonds: D:Y.33 Water bridges: D:L.18, D:L.18, D:Y.33 ACT.28: 5 residues within 4Å: Chain E: L.18, G.19, F.20, Y.33 Ligands: EDO.26 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:F.20, E:Y.33 Hydrogen bonds: E:Y.33 Water bridges: E:L.18, E:L.18, E:Y.33

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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