SMTL ID : 7vav.1

V1EG of V/A-ATPase from Thermus thermophilus at low ATP concentration, state3

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-2-2-mer

Ligands

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 15 residues within 4Å: Chain A: P.229, F.230, G.231, A.232, G.233, K.234, S.235, V.236, R.258, F.419, A.499, Y.500 Chain F: R.360, N.363 Ligands: MG.2 16 PLIP interactions: 13 interactions with chain A, 3 interactions with chain F Hydrogen bonds: A:G.231, A:A.232, A:G.233, A:K.234, A:S.235, A:V.236, A:R.258, A:A.499, A:Y.500, A:Y.500, F:N.363 Salt bridges: A:K.234, F:R.360, F:R.360 pi-Stacking: A:F.419, A:F.419

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: S.235, R.258 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.4: 5 residues within 4Å: Chain C: S.235, E.257, R.258, E.261 Ligands: ATP.3 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:S.235, C:E.261

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.3: 19 residues within 4Å: Chain C: P.229, F.230, G.231, A.232, G.233, K.234, S.235, V.236, E.257, R.258, F.419, Q.497, N.498, A.499 Chain E: G.330, Y.331, L.358, R.360 Ligands: MG.4 17 PLIP interactions: 4 interactions with chain E, 13 interactions with chain C Hydrogen bonds: E:Y.331, C:G.231, C:A.232, C:G.233, C:K.234, C:S.235, C:S.235, C:V.236, C:Q.497, C:A.499 Salt bridges: E:R.360, E:R.360, E:R.360, C:K.234, C:K.234, C:R.258 pi-Stacking: C:F.419

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kishikawa, J. et al., Structural snapshots of V/A-ATPase reveal the rotary catalytic mechanism of rotary ATPases. Nat Commun (2022)

Release Date

2022-07-13

Peptides

V-type ATP synthase alpha chain: ABC
V-type ATP synthase beta chain: DEF
V-type ATP synthase subunit D: G
V-type ATP synthase subunit F: H
V-type ATP synthase subunit G: IK
V-type ATP synthase subunit E: JL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

K
K

J
J

L
L

V-type ATP synthase alpha chain

V-type ATP synthase beta chain

V-type ATP synthase subunit D

V-type ATP synthase subunit F

V-type ATP synthase subunit G

V-type ATP synthase subunit E

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