SMTL ID : 1g6o.2 (1 other biounit)

CRYSTAL STRUCTURE OF THE HELICOBACTER PYLORI ATPASE, HP0525, IN COMPLEX WITH ADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-12-mer

Ligands

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

ADP.1: 14 residues within 4Å: Chain A: N.61, R.133, S.136, F.144, F.145, G.179, T.180, G.181, S.182, G.183, K.184, T.185, T.186, K.320 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:N.61, A:G.181, A:S.182, A:G.183, A:G.183, A:K.184, A:T.185, A:T.185, A:T.186, A:T.186 Water bridges: A:K.137, A:K.184, A:E.248, A:K.320 Salt bridges: A:R.133, A:R.133, A:K.184 pi-Stacking: A:Y.140 ADP.2: 16 residues within 4Å: Chain B: I.45, N.61, R.133, S.136, Y.140, F.144, F.145, G.179, T.180, G.181, S.182, G.183, K.184, T.185, T.186, K.320 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:I.45, B:N.61, B:R.133, B:G.181, B:S.182, B:G.183, B:K.184, B:T.185, B:T.185, B:T.186, B:T.186 Water bridges: B:K.137, B:T.185 Salt bridges: B:R.133, B:K.184 pi-Stacking: B:Y.140 pi-Cation interactions: B:K.320 ADP.8: 14 residues within 4Å: Chain C: N.61, R.133, S.136, F.144, F.145, G.179, T.180, G.181, S.182, G.183, K.184, T.185, T.186, K.320 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:N.61, C:G.181, C:S.182, C:G.183, C:G.183, C:K.184, C:T.185, C:T.185, C:T.186, C:T.186 Water bridges: C:K.137, C:K.184, C:E.248, C:K.320 Salt bridges: C:R.133, C:R.133, C:K.184 pi-Stacking: C:Y.140 ADP.9: 16 residues within 4Å: Chain D: I.45, N.61, R.133, S.136, Y.140, F.144, F.145, G.179, T.180, G.181, S.182, G.183, K.184, T.185, T.186, K.320 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:I.45, D:N.61, D:R.133, D:G.181, D:S.182, D:G.183, D:K.184, D:T.185, D:T.185, D:T.186, D:T.186 Water bridges: D:K.137, D:T.185 Salt bridges: D:R.133, D:K.184 pi-Stacking: D:Y.140 pi-Cation interactions: D:K.320 ADP.15: 14 residues within 4Å: Chain E: N.61, R.133, S.136, F.144, F.145, G.179, T.180, G.181, S.182, G.183, K.184, T.185, T.186, K.320 18 PLIP interactions: 18 interactions with chain E Hydrogen bonds: E:N.61, E:G.181, E:S.182, E:G.183, E:G.183, E:K.184, E:T.185, E:T.185, E:T.186, E:T.186 Water bridges: E:K.137, E:K.184, E:E.248, E:K.320 Salt bridges: E:R.133, E:R.133, E:K.184 pi-Stacking: E:Y.140 ADP.16: 16 residues within 4Å: Chain F: I.45, N.61, R.133, S.136, Y.140, F.144, F.145, G.179, T.180, G.181, S.182, G.183, K.184, T.185, T.186, K.320 17 PLIP interactions: 17 interactions with chain F Hydrogen bonds: F:I.45, F:N.61, F:R.133, F:G.181, F:S.182, F:G.183, F:K.184, F:T.185, F:T.185, F:T.186, F:T.186 Water bridges: F:K.137, F:T.185 Salt bridges: F:R.133, F:K.184 pi-Stacking: F:Y.140 pi-Cation interactions: F:K.320 ADP.22: 14 residues within 4Å: Chain G: N.61, R.133, S.136, F.144, F.145, G.179, T.180, G.181, S.182, G.183, K.184, T.185, T.186, K.320 18 PLIP interactions: 18 interactions with chain G Hydrogen bonds: G:N.61, G:G.181, G:S.182, G:G.183, G:G.183, G:K.184, G:T.185, G:T.186, G:T.186 Water bridges: G:K.137, G:K.184, G:T.185, G:E.248, G:K.320 Salt bridges: G:R.133, G:R.133, G:K.184 pi-Stacking: G:Y.140 ADP.23: 16 residues within 4Å: Chain H: I.45, N.61, R.133, S.136, Y.140, F.144, F.145, G.179, T.180, G.181, S.182, G.183, K.184, T.185, T.186, K.320 17 PLIP interactions: 17 interactions with chain H Hydrogen bonds: H:I.45, H:N.61, H:R.133, H:Y.140, H:G.181, H:S.182, H:G.183, H:K.184, H:T.185, H:T.186, H:T.186 Water bridges: H:K.137, H:T.185 Salt bridges: H:R.133, H:K.184 pi-Stacking: H:Y.140 pi-Cation interactions: H:K.320 ADP.29: 14 residues within 4Å: Chain I: N.61, R.133, S.136, F.144, F.145, G.179, T.180, G.181, S.182, G.183, K.184, T.185, T.186, K.320 18 PLIP interactions: 18 interactions with chain I Hydrogen bonds: I:N.61, I:G.181, I:S.182, I:G.183, I:G.183, I:K.184, I:T.185, I:T.186, I:T.186 Water bridges: I:K.137, I:K.184, I:T.185, I:E.248, I:K.320 Salt bridges: I:R.133, I:R.133, I:K.184 pi-Stacking: I:Y.140 ADP.30: 16 residues within 4Å: Chain J: I.45, N.61, R.133, S.136, Y.140, F.144, F.145, G.179, T.180, G.181, S.182, G.183, K.184, T.185, T.186, K.320 17 PLIP interactions: 17 interactions with chain J Hydrogen bonds: J:I.45, J:N.61, J:R.133, J:Y.140, J:G.181, J:S.182, J:G.183, J:K.184, J:T.185, J:T.186, J:T.186 Water bridges: J:K.137, J:T.185 Salt bridges: J:R.133, J:K.184 pi-Stacking: J:Y.140 pi-Cation interactions: J:K.320 ADP.36: 14 residues within 4Å: Chain K: N.61, R.133, S.136, F.144, F.145, G.179, T.180, G.181, S.182, G.183, K.184, T.185, T.186, K.320 18 PLIP interactions: 18 interactions with chain K Hydrogen bonds: K:N.61, K:G.181, K:S.182, K:G.183, K:G.183, K:K.184, K:T.185, K:T.186, K:T.186 Water bridges: K:K.137, K:K.184, K:T.185, K:E.248, K:K.320 Salt bridges: K:R.133, K:R.133, K:K.184 pi-Stacking: K:Y.140 ADP.37: 16 residues within 4Å: Chain L: I.45, N.61, R.133, S.136, Y.140, F.144, F.145, G.179, T.180, G.181, S.182, G.183, K.184, T.185, T.186, K.320 17 PLIP interactions: 17 interactions with chain L Hydrogen bonds: L:I.45, L:N.61, L:R.133, L:Y.140, L:G.181, L:S.182, L:G.183, L:K.184, L:T.185, L:T.186, L:T.186 Water bridges: L:K.137, L:T.185 Salt bridges: L:R.133, L:K.184 pi-Stacking: L:Y.140 pi-Cation interactions: L:K.320

30 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 4 residues within 4Å: Chain B: P.67, F.68, D.69 Ligands: PEG.4 Ligand excluded by PLIP PEG.4: 6 residues within 4Å: Chain B: F.39, F.68, D.69, R.73 Ligands: PEG.3, PEG.5 Ligand excluded by PLIP PEG.5: 3 residues within 4Å: Chain B: D.38 Ligands: PEG.4, PEG.6 Ligand excluded by PLIP PEG.6: 4 residues within 4Å: Chain B: D.38, K.41 Ligands: PEG.5, PEG.7 Ligand excluded by PLIP PEG.7: 2 residues within 4Å: Chain B: E.43 Ligands: PEG.6 Ligand excluded by PLIP PEG.10: 4 residues within 4Å: Chain D: P.67, F.68, D.69 Ligands: PEG.11 Ligand excluded by PLIP PEG.11: 6 residues within 4Å: Chain D: F.39, F.68, D.69, R.73 Ligands: PEG.10, PEG.12 Ligand excluded by PLIP PEG.12: 3 residues within 4Å: Chain D: D.38 Ligands: PEG.11, PEG.13 Ligand excluded by PLIP PEG.13: 4 residues within 4Å: Chain D: D.38, K.41 Ligands: PEG.12, PEG.14 Ligand excluded by PLIP PEG.14: 2 residues within 4Å: Chain D: E.43 Ligands: PEG.13 Ligand excluded by PLIP PEG.17: 4 residues within 4Å: Chain F: P.67, F.68, D.69 Ligands: PEG.18 Ligand excluded by PLIP PEG.18: 6 residues within 4Å: Chain F: F.39, F.68, D.69, R.73 Ligands: PEG.17, PEG.19 Ligand excluded by PLIP PEG.19: 3 residues within 4Å: Chain F: D.38 Ligands: PEG.18, PEG.20 Ligand excluded by PLIP PEG.20: 4 residues within 4Å: Chain F: D.38, K.41 Ligands: PEG.19, PEG.21 Ligand excluded by PLIP PEG.21: 2 residues within 4Å: Chain F: E.43 Ligands: PEG.20 Ligand excluded by PLIP PEG.24: 4 residues within 4Å: Chain H: P.67, F.68, D.69 Ligands: PEG.25 Ligand excluded by PLIP PEG.25: 6 residues within 4Å: Chain H: F.39, F.68, D.69, R.73 Ligands: PEG.24, PEG.26 Ligand excluded by PLIP PEG.26: 3 residues within 4Å: Chain H: D.38 Ligands: PEG.25, PEG.27 Ligand excluded by PLIP PEG.27: 4 residues within 4Å: Chain H: D.38, K.41 Ligands: PEG.26, PEG.28 Ligand excluded by PLIP PEG.28: 2 residues within 4Å: Chain H: E.43 Ligands: PEG.27 Ligand excluded by PLIP PEG.31: 4 residues within 4Å: Chain J: P.67, F.68, D.69 Ligands: PEG.32 Ligand excluded by PLIP PEG.32: 6 residues within 4Å: Chain J: F.39, F.68, D.69, R.73 Ligands: PEG.31, PEG.33 Ligand excluded by PLIP PEG.33: 3 residues within 4Å: Chain J: D.38 Ligands: PEG.32, PEG.34 Ligand excluded by PLIP PEG.34: 4 residues within 4Å: Chain J: D.38, K.41 Ligands: PEG.33, PEG.35 Ligand excluded by PLIP PEG.35: 2 residues within 4Å: Chain J: E.43 Ligands: PEG.34 Ligand excluded by PLIP PEG.38: 4 residues within 4Å: Chain L: P.67, F.68, D.69 Ligands: PEG.39 Ligand excluded by PLIP PEG.39: 6 residues within 4Å: Chain L: F.39, F.68, D.69, R.73 Ligands: PEG.38, PEG.40 Ligand excluded by PLIP PEG.40: 3 residues within 4Å: Chain L: D.38 Ligands: PEG.39, PEG.41 Ligand excluded by PLIP PEG.41: 4 residues within 4Å: Chain L: D.38, K.41 Ligands: PEG.40, PEG.42 Ligand excluded by PLIP PEG.42: 2 residues within 4Å: Chain L: E.43 Ligands: PEG.41 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yeo, H.J. et al., Crystal structure of the hexameric traffic ATPase of the Helicobacter pylori type IV secretion system. Mol.Cell (2000)

Release Date

2001-01-24

Peptides

CAG-ALPHA: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

I
A

J
B

K
A

L
B

CAG-ALPHA

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