SMTL ID : 5knd.1

Crystal structure of the Pi-bound V1 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.89 Å

Oligo State

hetero-3-3-1-1-mer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain C: T.246, E.268, D.336 Ligands: PO4.3 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.246, H2O.2, H2O.2, H2O.2

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain C: M.34, L.78, S.79, I.94 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.79, C:I.94 GOL.4: 4 residues within 4Å: Chain F: D.179, G.366, K.367, T.368 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:D.179, F:T.368 GOL.6: 1 residues within 4Å: Chain G: T.188 No protein-ligand interaction detected (PLIP)

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 11 residues within 4Å: Chain C: F.241, G.242, K.245, T.246, E.268, R.269, S.398 Chain F: G.327, Y.328, R.357 Ligands: MG.1 12 PLIP interactions: 10 interactions with chain C, 2 interactions with chain F Hydrogen bonds: C:G.242, C:E.268, C:S.398 Water bridges: C:G.244, C:K.245, C:R.340, C:R.340, C:R.340, F:R.357 Salt bridges: C:K.245, C:R.269, F:R.357

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

B3P.5: 5 residues within 4Å: Chain F: E.90, D.183, R.213, K.246, M.248 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:E.90, F:D.183

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Suzuki, K. et al., Crystal structures of the ATP-binding and ADP-release dwells of the V1 rotary motor. Nat Commun (2016)

Release Date

2016-11-02

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 NtpG (F): 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 NtpG (F)

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