SMTL ID : 3vr3.1

Crystal structure of AMP-PNP bound A3B3 complex from Enterococcus hirae V-ATPase [bA3B3]

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.40 Å

Oligo State

hetero-3-3-mer

Ligands

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

ANP.1: 18 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 Chain E: G.327, Y.328, R.357 Ligands: MG.2 20 PLIP interactions: 14 interactions with chain B, 6 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, E:K.359 pi-Stacking: B:F.432 Water bridges: E:D.360 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, P.433, Q.510, N.511, A.512 Chain F: G.327, Y.328, L.355, R.357 Ligands: MG.4 21 PLIP interactions: 7 interactions with chain F, 14 interactions with chain C Hydrogen bonds: F:Y.328, F:R.357, F:R.357, F:K.359, 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 Water bridges: F:R.357, F:K.359 Salt bridges: F:R.357 pi-Stacking: C:F.432

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain B: T.246, E.268, R.269, E.272 Ligands: ANP.1 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.246 MG.4: 5 residues within 4Å: Chain C: T.246, E.268, R.269, E.272 Ligands: ANP.3 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.246

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

V-type sodium ATPase catalytic subunit A

V-type sodium ATPase subunit B

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