SMTL ID : 6bge.1

HELICOBACTER PYLORI ATPASE, HP0525, IN COMPLEX WITH 1G2 COMPOUND

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-hexamer

Ligands

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 7 residues within 4Å: Chain A: R.128, G.174, G.176, S.177, G.178, K.179, T.180 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.176, A:S.177, A:G.178, A:K.179, A:T.180, A:T.180 Salt bridges: A:R.128, A:K.179 SO4.2: 6 residues within 4Å: Chain A: N.39, N.56, S.131, K.132, T.133, Y.135 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.39, A:N.56, A:S.131, A:K.132, A:T.133, A:T.133 SO4.5: 7 residues within 4Å: Chain B: R.128, G.174, G.176, S.177, G.178, K.179, T.180 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.176, B:S.177, B:G.178, B:K.179, B:T.180, B:T.180 Salt bridges: B:R.128, B:K.179 SO4.6: 6 residues within 4Å: Chain B: N.39, N.56, S.131, K.132, T.133, Y.135 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.39, B:N.56, B:S.131, B:K.132, B:T.133, B:T.133 SO4.9: 7 residues within 4Å: Chain C: R.128, G.174, G.176, S.177, G.178, K.179, T.180 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:G.176, C:S.177, C:G.178, C:K.179, C:T.180, C:T.180 Salt bridges: C:R.128, C:K.179 SO4.10: 6 residues within 4Å: Chain C: N.39, N.56, S.131, K.132, T.133, Y.135 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.39, C:N.56, C:S.131, C:K.132, C:T.133, C:T.133 SO4.14: 7 residues within 4Å: Chain D: R.128, G.174, G.176, S.177, G.178, K.179, T.180 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:G.176, D:S.177, D:G.178, D:K.179, D:T.180, D:T.180 Salt bridges: D:R.128, D:K.179 SO4.15: 6 residues within 4Å: Chain D: N.39, N.56, S.131, K.132, T.133, Y.135 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:N.39, D:N.39, D:N.56, D:S.131, D:K.132, D:T.133 Water bridges: D:K.132 SO4.18: 7 residues within 4Å: Chain E: R.128, G.174, G.176, S.177, G.178, K.179, T.180 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:G.176, E:S.177, E:G.178, E:K.179, E:T.180, E:T.180 Salt bridges: E:R.128, E:K.179 SO4.19: 6 residues within 4Å: Chain E: N.39, N.56, S.131, K.132, T.133, Y.135 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:N.39, E:N.39, E:N.56, E:S.131, E:K.132, E:T.133 Water bridges: E:K.132 SO4.22: 7 residues within 4Å: Chain F: R.128, G.174, G.176, S.177, G.178, K.179, T.180 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:G.176, F:S.177, F:G.178, F:K.179, F:T.180, F:T.180 Salt bridges: F:R.128, F:K.179 SO4.23: 6 residues within 4Å: Chain F: N.39, N.56, S.131, K.132, T.133, Y.135 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:N.39, F:N.39, F:N.56, F:S.131, F:K.132, F:T.133 Water bridges: F:K.132

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: F.86, K.87, K.88 Chain F: P.115 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.87 GOL.7: 4 residues within 4Å: Chain B: F.86, K.87, K.88 Chain D: P.115 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.87 GOL.11: 4 residues within 4Å: Chain C: F.86, K.87, K.88 Chain E: P.115 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.87 GOL.16: 4 residues within 4Å: Chain D: D.67, R.68, K.69, A.70 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.69, D:A.70 GOL.20: 4 residues within 4Å: Chain E: D.67, R.68, K.69, A.70 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.69, E:A.70 GOL.24: 4 residues within 4Å: Chain F: D.67, R.68, K.69, A.70 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:K.69, F:A.70

3 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.4: 3 residues within 4Å: Chain A: K.192, E.193, K.211 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.192, A:K.211, A:N.212 Salt bridges: A:K.192 EPE.8: 3 residues within 4Å: Chain B: K.192, E.193, K.211 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.192, B:K.211, B:N.212 Salt bridges: B:K.192 EPE.12: 3 residues within 4Å: Chain C: K.192, E.193, K.211 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.192, C:K.211, C:N.212 Salt bridges: C:K.192

3 x DN7: 4-[(pyridin-2-yl)oxy]benzoic acid(Non-covalent)

DN7.13: 5 residues within 4Å: Chain D: D.33, M.37, F.63, D.64, R.68 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:D.33, D:F.63 Hydrogen bonds: D:D.64, D:R.68 DN7.17: 5 residues within 4Å: Chain E: D.33, M.37, F.63, D.64, R.68 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:D.33, E:F.63 Hydrogen bonds: E:D.64, E:R.68 DN7.21: 5 residues within 4Å: Chain F: D.33, M.37, F.63, D.64, R.68 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:D.33, F:F.63 Hydrogen bonds: F:D.64, F:R.68

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arya, T. et al., CagAlpha in complex with hexamer inhibitor. To Be Published

Release Date

2018-10-31

Peptides

VirB11-like protein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
B

E
B

F
B

VirB11-like protein