SMTL ID : 6iud.1

Structure of Helicobacter pylori Soj-ADP complex bound to DNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.51 Å

Oligo State

homo-tetramer

Ligands

4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 17 residues within 4Å: Chain A: G.26, V.27, G.28, K.29, T.30, T.31, N.57, M.202, I.237, P.238, K.239, S.240, L.243, A.244 Chain B: K.24, E.168 Ligands: MG.2 15 PLIP interactions: 12 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:G.26, A:V.27, A:G.28, A:K.29, A:T.30, A:T.31, A:T.31, A:N.57, A:M.202, A:P.238, A:S.240, B:E.168 Salt bridges: A:K.29, B:K.24, B:K.24 ADP.3: 18 residues within 4Å: Chain A: K.24, E.168, F.170 Chain B: G.25, G.26, V.27, G.28, K.29, T.30, T.31, M.202, I.237, P.238, K.239, S.240, L.243, A.244 Ligands: MG.4 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:G.26, B:V.27, B:G.28, B:K.29, B:T.30, B:T.31, B:T.31, B:M.202, B:P.238, B:S.240, A:E.168 Salt bridges: B:K.29, A:K.24, A:K.24 ADP.5: 16 residues within 4Å: Chain C: G.26, V.27, G.28, K.29, T.30, T.31, M.202, I.237, P.238, K.239, S.240, L.243, A.244 Chain D: K.24, E.168 Ligands: MG.6 15 PLIP interactions: 11 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:G.26, C:V.27, C:G.28, C:K.29, C:T.30, C:T.31, C:T.31, C:M.202, C:P.238, C:S.240, D:E.168, D:E.168 Salt bridges: C:K.29, D:K.24, D:K.24 ADP.7: 18 residues within 4Å: Chain C: K.24, E.168, F.170 Chain D: G.25, G.26, V.27, G.28, K.29, T.30, T.31, M.202, I.237, P.238, K.239, S.240, L.243, A.244 Ligands: MG.8 13 PLIP interactions: 11 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:G.26, D:V.27, D:G.28, D:K.29, D:T.30, D:T.31, D:T.31, D:M.202, D:P.238, D:S.240 Salt bridges: D:K.29, C:K.24, C:K.24

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.30, D.53, Q.55 Ligands: ADP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.30 MG.4: 4 residues within 4Å: Chain B: T.30, D.53, D.142 Ligands: ADP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.30 MG.6: 4 residues within 4Å: Chain C: T.30, D.53, N.57 Ligands: ADP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.30 MG.8: 4 residues within 4Å: Chain D: K.29, T.30, D.53 Ligands: ADP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.30

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chu, C.H. et al., Crystal structures of HpSoj-DNA complexes and the nucleoid-adaptor complex formation in chromosome segregation. Nucleic Acids Res. (2019)

Release Date

2019-02-13

Peptides

SpoOJ regulator (Soj): ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

SpoOJ regulator (Soj)

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