SMTL ID : 3vr4.1

Crystal structure of Enterococcus hirae V1-ATPase [eV1]

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

hetero-3-3-1-1-mer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: H.250, Q.251, K.254, L.283, F.513 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.250, A:Q.251, A:K.254 GOL.3: 5 residues within 4Å: Chain B: D.423, L.426, N.436, W.437, I.438 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.437, B:W.437 GOL.4: 3 residues within 4Å: Chain D: H.82, Q.85, Y.115 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.85 Water bridges: D:Q.85 GOL.5: 1 residues within 4Å: Chain D: Y.425 No protein-ligand interaction detected (PLIP) GOL.8: 3 residues within 4Å: Chain F: T.176, D.182, D.183 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:S.180 Water bridges: F:T.176, F:D.183, F:R.213 GOL.9: 4 residues within 4Å: Chain F: E.245, K.246, G.247 Ligands: B3P.6 No protein-ligand interaction detected (PLIP) GOL.10: 4 residues within 4Å: Chain F: D.179, G.366, K.367, T.368 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:T.368 GOL.11: 1 residues within 4Å: Chain G: T.188 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:Q.184

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 4 residues within 4Å: Chain B: F.241, G.242, R.269 Chain E: R.357 Ligand excluded by PLIP

2 x B3P: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

B3P.6: 6 residues within 4Å: Chain F: E.90, D.183, R.213, K.246, M.248 Ligands: GOL.9 4 PLIP interactions: 4 interactions with chain F Water bridges: F:D.183, F:D.183, F:D.183, F:D.183 B3P.7: 7 residues within 4Å: Chain C: N.278 Chain F: D.129, Y.130, D.132, E.133, R.297, R.299 11 PLIP interactions: 10 interactions with chain F, 1 interactions with chain C Hydrogen bonds: F:D.129, F:D.129, F:Y.130, F:Y.130, F:R.299, C:N.278 Water bridges: F:D.129, F:D.132, F:D.132, F:R.297, F:L.301

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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