SMTL ID : 8gxz.1

1 sulfate and 1 ATP 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 SO4: SULFATE ION(Non-functional Binders)

SO4.1: 8 residues within 4Å: Chain A: P.229, G.231, A.232, G.233, K.234, S.235, R.258 Chain F: R.360 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:G.231, A:A.232, A:G.233, A:K.234, A:S.235 Salt bridges: A:K.234, A:R.258, F:R.360

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

ATP.2: 17 residues within 4Å: Chain C: F.230, G.231, A.232, G.233, K.234, S.235, V.236, R.258, F.419, Q.497, A.499, Y.500 Chain E: G.330, Y.331, L.358, R.360 Ligands: MG.3 19 PLIP interactions: 15 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:S.235, C:V.236, C:Q.497, C:A.499, C:Y.500, C:Y.500, E:G.330 Salt bridges: C:R.258, E:R.360, E:R.360, E:R.360 pi-Stacking: C:F.419

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain C: K.234, S.235 Ligands: ATP.2 No protein-ligand interaction detected (PLIP)

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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