SMTL ID : 8igv.1

Hexameric Ring Complex of Engineered V1-ATPase bound to 5 ADPs: A3(De)3_(ADP-Pi)1cat(ADP)2cat,2non-cat

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.15 Å

Oligo State

hetero-3-3-mer

Ligands

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

ADP.1: 17 residues within 4Å: Chain A: P.236, F.237, G.238, A.239, G.240, K.241, T.242, V.243, R.426, F.428, Q.506, N.507, A.508, F.509 Chain D: R.350 Ligands: MG.2, PO4.3 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:G.238, A:K.241, A:T.242, A:T.242, A:V.243, A:R.426, A:Q.506, A:A.508 Salt bridges: A:K.241, D:R.350 Water bridges: D:D.353 ADP.4: 15 residues within 4Å: Chain B: P.236, F.237, G.238, A.239, G.240, K.241, T.242, V.243, F.428, P.429, Q.506, N.507, A.508, F.509 Ligands: MG.5 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.238, B:A.239, B:G.240, B:T.242, B:V.243, B:Q.506, B:A.508 Salt bridges: B:K.241 ADP.6: 16 residues within 4Å: Chain C: P.236, F.237, G.238, A.239, G.240, K.241, T.242, V.243, R.265, E.268, F.428, Q.506, N.507, A.508, F.509 Ligands: MG.7 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:G.238, C:A.239, C:K.241, C:T.242, C:T.242, C:V.243, C:R.265, C:Q.506, C:A.508 Salt bridges: C:K.241 pi-Stacking: C:F.428 ADP.8: 17 residues within 4Å: Chain C: L.409, R.410, V.412, K.413, Y.437, L.439 Chain D: P.152, P.153, G.154, A.155, G.156, K.157, S.158, E.190, T.305, R.331 Ligands: MG.9 12 PLIP interactions: 9 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:G.154, D:A.155, D:G.156, D:K.157, D:S.158, D:T.305, D:R.331, C:R.410 Salt bridges: D:K.157, D:K.157 pi-Stacking: C:Y.437, C:Y.437 ADP.10: 14 residues within 4Å: Chain A: L.409, R.410, V.412, Y.437, L.439 Chain E: P.153, G.154, A.155, G.156, K.157, S.158, A.159, E.190 Ligands: MG.11 11 PLIP interactions: 8 interactions with chain E, 3 interactions with chain A Hydrogen bonds: E:G.154, E:A.155, E:G.156, E:K.157, E:S.158, E:A.159, E:E.190, E:E.248, A:V.412 pi-Stacking: A:Y.437, A:Y.437

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: T.242, R.265, E.268, D.332 Ligands: ADP.1, PO4.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.242 MG.5: 5 residues within 4Å: Chain B: T.242, E.264, E.268, D.332 Ligands: ADP.4 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.242, B:E.268 MG.7: 6 residues within 4Å: Chain C: T.242, E.264, R.265, E.268, D.332 Ligands: ADP.6 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.242 MG.9: 4 residues within 4Å: Chain D: S.158, E.190, E.248 Ligands: ADP.8 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:S.158, D:E.190, D:E.248 MG.11: 3 residues within 4Å: Chain E: S.158, E.190 Ligands: ADP.10 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:S.158, E:E.190

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

PO4.3: 9 residues within 4Å: Chain A: F.237, K.241, T.242, R.265, R.336, S.394 Chain D: R.350 Ligands: ADP.1, MG.2 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:S.394, A:S.394 Salt bridges: A:K.241, A:R.265, A:R.336, D:R.350

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kosugi, T. et al., Design of allosteric sites into rotary motor V 1 -ATPase by restoring lost function of pseudo-active sites. Nat.Chem. (2023)

Release Date

2023-07-12

Peptides

V-type sodium ATPase catalytic subunit A: ABC
V-type sodium ATPase subunit B: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

V-type sodium ATPase catalytic subunit A

V-type sodium ATPase subunit B

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