SMTL ID : 6fj5.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 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.9: 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.14: 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

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

EDO.2: 4 residues within 4Å: Chain A: T.138, H.140 Chain B: S.2, V.4 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Water bridges: A:T.138, A:T.138, B:S.2 Hydrogen bonds: B:S.2 EDO.3: 5 residues within 4Å: Chain A: K.39, S.147, P.157, V.179, R.180 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:K.39, A:S.147, A:E.178, A:V.179, A:R.180 Water bridges: A:K.39, A:I.158, A:R.180, A:E.192 EDO.4: 2 residues within 4Å: Chain A: S.2, V.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.2 EDO.6: 6 residues within 4Å: Chain B: K.39, S.147, P.157, E.178, V.179, R.180 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.39, B:E.178, B:V.179, B:R.180, B:E.192 Water bridges: B:I.158 EDO.7: 6 residues within 4Å: Chain B: F.20, L.21, C.31, T.32, Y.33, P.49 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.21, B:C.31, B:P.49 EDO.8: 6 residues within 4Å: Chain B: V.104, E.105, G.106, T.138, I.139, H.140 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.106, B:H.140, B:H.140 EDO.10: 3 residues within 4Å: Chain C: R.17, L.18, W.53 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:W.53 EDO.11: 7 residues within 4Å: Chain C: F.20, L.21, C.31, T.32, Y.33, M.40, P.49 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:L.21, C:C.31, C:P.49 Water bridges: C:Y.33 EDO.12: 6 residues within 4Å: Chain C: K.39, S.147, P.157, V.179, R.180, E.192 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:K.39, C:S.147, C:V.179, C:R.180, C:E.192 Water bridges: C:I.158 EDO.13: 5 residues within 4Å: Chain C: P.5, S.6, Q.7, I.69, M.76 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.7 EDO.15: 3 residues within 4Å: Chain D: R.17, L.18, W.53 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:W.53 EDO.16: 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.17: 6 residues within 4Å: Chain D: K.39, S.147, P.157, V.179, R.180, E.192 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:K.39, D:S.147, D:V.179, D:R.180, D:E.192 Water bridges: D:I.158 EDO.18: 5 residues within 4Å: Chain D: P.5, S.6, Q.7, I.69, M.76 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:P.5, D:Q.7

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

2018-06-27

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

Related Entries With Identical Sequence