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

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-hexamer

Ligands

6 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

15 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 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.69 PEG.4: 6 residues within 4Å: Chain B: F.39, F.68, D.69, R.73 Ligands: PEG.3, PEG.5 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.68 PEG.5: 3 residues within 4Å: Chain B: D.38 Ligands: PEG.4, PEG.6 No protein-ligand interaction detected (PLIP) PEG.6: 4 residues within 4Å: Chain B: D.38, K.41 Ligands: PEG.5, PEG.7 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:K.41 Water bridges: B:E.43 PEG.7: 2 residues within 4Å: Chain B: E.43 Ligands: PEG.6 No protein-ligand interaction detected (PLIP) PEG.10: 4 residues within 4Å: Chain D: P.67, F.68, D.69 Ligands: PEG.11 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.69 PEG.11: 6 residues within 4Å: Chain D: F.39, F.68, D.69, R.73 Ligands: PEG.10, PEG.12 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:F.68 PEG.12: 3 residues within 4Å: Chain D: D.38 Ligands: PEG.11, PEG.13 No protein-ligand interaction detected (PLIP) PEG.13: 4 residues within 4Å: Chain D: D.38, K.41 Ligands: PEG.12, PEG.14 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:K.41 Water bridges: D:E.43 PEG.14: 2 residues within 4Å: Chain D: E.43 Ligands: PEG.13 No protein-ligand interaction detected (PLIP) PEG.17: 4 residues within 4Å: Chain F: P.67, F.68, D.69 Ligands: PEG.18 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:D.69 PEG.18: 6 residues within 4Å: Chain F: F.39, F.68, D.69, R.73 Ligands: PEG.17, PEG.19 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:F.68 PEG.19: 3 residues within 4Å: Chain F: D.38 Ligands: PEG.18, PEG.20 No protein-ligand interaction detected (PLIP) PEG.20: 4 residues within 4Å: Chain F: D.38, K.41 Ligands: PEG.19, PEG.21 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:K.41 Water bridges: F:E.43 PEG.21: 2 residues within 4Å: Chain F: E.43 Ligands: PEG.20 No protein-ligand interaction detected (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: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

CAG-ALPHA

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