SMTL ID : 8gxx.1

3 nucleotide-bound V1EG of V/A-ATPase from Thermus thermophilus.

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: 16 residues within 4Å: Chain A: P.229, F.230, G.231, A.232, G.233, K.234, S.235, V.236, F.419, Q.497, N.498, A.499 Chain F: L.358, R.360, N.363 Ligands: MG.2 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain F Hydrogen bonds: A:G.231, A:G.233, A:K.234, A:S.235, A:S.235, A:V.236, A:Q.497, A:A.499, F:N.363 Salt bridges: A:K.234, F:R.360, F:R.360 pi-Stacking: A:F.419

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: S.235, E.257, R.258 Ligands: ADP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.235 MG.5: 4 residues within 4Å: Chain C: S.235, R.258, E.261 Ligands: ATP.4 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:S.235, C:E.261

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

ATP.3: 14 residues within 4Å: Chain B: P.229, F.230, G.231, A.232, G.233, K.234, S.235, V.236, F.419, Q.497, N.498, A.499, Y.500 Chain D: R.360 18 PLIP interactions: 17 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:P.229, B:G.231, B:A.232, B:G.233, B:K.234, B:S.235, B:S.235, B:S.235, B:V.236, B:E.261, B:Q.497, B:A.499, B:Y.500 Salt bridges: B:K.234, B:K.234, B:R.258, D:R.360 pi-Stacking: B:F.419 ATP.4: 18 residues within 4Å: Chain C: 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, Y.500 Chain E: G.330, Y.331, R.360 Ligands: MG.5 18 PLIP interactions: 14 interactions with chain C, 4 interactions with chain E Hydrogen bonds: C:P.229, 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, E:Y.331 Salt bridges: C:K.234, C:K.234, C:R.258, E:R.360, E:R.360, E:R.360 pi-Stacking: C:F.419

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakanishi, A. et al., Cryo-EM analysis of V/A-ATPase intermediates reveals the transition of the ground-state structure to steady-state structures by sequential ATP binding. J.Biol.Chem. (2023)

Release Date

2023-01-25

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 (VAPC-THERM): 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 (VAPC-THERM)

V-type ATP synthase subunit E

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