SMTL ID : 3vr6.1

Crystal structure of AMP-PNP bound Enterococcus hirae V1-ATPase [bV1]

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.68 Å

Oligo State

hetero-3-3-1-1-mer

Ligands

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 19 residues within 4Å: Chain B: P.240, F.241, G.242, A.243, G.244, K.245, T.246, V.247, E.268, R.269, F.432, Q.510, N.511, A.512, F.513 Chain E: G.327, Y.328, R.357 Ligands: MG.2 19 PLIP interactions: 15 interactions with chain B, 4 interactions with chain E Hydrogen bonds: B:G.242, B:A.243, B:G.244, B:K.245, B:K.245, B:K.245, B:T.246, B:T.246, B:V.247, B:R.269, B:R.269, B:Q.510, B:A.512, E:Y.328, E:R.357, E:R.357 Water bridges: B:E.268 pi-Stacking: B:F.432 Salt bridges: E:R.357 ANP.3: 20 residues within 4Å: Chain C: P.240, F.241, G.242, A.243, G.244, K.245, T.246, V.247, E.268, R.269, F.432, N.511, A.512, F.513 Chain F: Y.328, L.355, S.356, R.357, K.359 Ligands: MG.4 24 PLIP interactions: 17 interactions with chain C, 7 interactions with chain F Hydrogen bonds: C:G.242, C:A.243, C:G.244, C:K.245, C:K.245, C:K.245, C:T.246, C:T.246, C:V.247, C:R.269, C:R.269, C:Q.510, C:A.512, F:Y.328, F:R.357, F:R.357, F:K.359 Water bridges: C:R.340, C:R.340, F:R.357, F:K.359 pi-Stacking: C:F.432, C:F.432 Salt bridges: F:R.357

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain B: T.246, R.269 Ligands: ANP.1 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.246, H2O.5, H2O.5, H2O.5 MG.4: 4 residues within 4Å: Chain C: T.246, E.268, R.269 Ligands: ANP.3 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.246, H2O.9, H2O.9, H2O.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arai, S. et al., Rotation mechanism of Enterococcus hirae V(1)-ATPase based on asymmetric crystal structures. Nature (2013)

Release Date

2013-01-16

Peptides

V-type sodium ATPase catalytic subunit A: ABC
V-type sodium ATPase subunit B: DEF
V-type sodium ATPase subunit D: G
V-type sodium ATPase subunit G: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

V-type sodium ATPase catalytic subunit A

V-type sodium ATPase subunit B

V-type sodium ATPase subunit D

V-type sodium ATPase subunit G

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