SMTL ID : 8wci.1

Cryo-EM structure of the inhibitor-bound Vo complex from Enterococcus hirae

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-10-1-mer

Ligands

5 x CDL: CARDIOLIPIN(Non-covalent)

CDL.1: 17 residues within 4Å: Chain A: T.21, F.25, F.101, L.104, F.105, I.108 Chain B: T.21, I.24, F.25, I.28, K.32, L.97, L.104, F.105, I.108 Chain J: F.101, F.105 20 PLIP interactions: 3 interactions with chain J, 7 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: J:F.101, J:F.101, J:F.101, A:F.25, A:F.25, A:F.101, A:F.101, A:L.104, A:F.105, B:I.24, B:F.25, B:F.25, B:F.25, B:I.28, B:L.97, B:F.105 Salt bridges: A:K.32, B:K.32, B:K.32, B:K.32 CDL.5: 19 residues within 4Å: Chain B: F.101, F.105 Chain C: L.17, T.21, I.24, F.25, I.28, K.32, F.101, F.105, I.108 Chain D: L.17, T.21, F.25, K.32, F.101, L.104, F.105, I.108 17 PLIP interactions: 9 interactions with chain C, 5 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: C:L.17, C:I.24, C:I.24, C:F.101, C:F.101, C:F.105, C:F.105, D:L.17, D:F.101, B:F.101, B:F.101, B:F.101 Salt bridges: C:K.32, C:K.112, D:K.32, D:K.32, D:K.32 CDL.8: 22 residues within 4Å: Chain D: L.97, F.101, F.105 Chain E: A.20, T.21, I.24, F.25, I.28, K.32, L.97, F.101, F.105, I.108 Chain F: T.21, I.24, F.25, I.28, K.32, F.101, L.104, F.105, I.108 30 PLIP interactions: 15 interactions with chain E, 9 interactions with chain F, 6 interactions with chain D Hydrophobic interactions: E:A.20, E:I.24, E:F.25, E:F.25, E:F.25, E:I.28, E:L.97, E:F.101, E:F.101, E:F.101, E:F.101, E:F.105, E:F.105, F:I.24, F:F.25, F:I.28, F:F.101, F:L.104, F:F.105, D:L.97, D:F.101, D:F.101, D:F.101, D:F.105, D:F.105 Salt bridges: E:K.32, E:K.112, F:K.32, F:K.32, F:K.32 CDL.10: 21 residues within 4Å: Chain F: L.97, F.101, F.105 Chain G: T.21, I.24, F.25, K.32, F.101, L.104, F.105, I.108 Chain H: T.21, I.24, F.25, I.28, K.32, L.97, F.101, L.104, F.105, I.108 20 PLIP interactions: 10 interactions with chain H, 3 interactions with chain F, 7 interactions with chain G Hydrophobic interactions: H:I.24, H:F.25, H:I.28, H:L.97, H:F.101, H:F.101, H:F.105, F:L.97, F:F.101, F:F.105, G:I.24, G:F.101, G:L.104, G:F.105 Salt bridges: H:K.32, H:K.32, H:K.32, G:K.32, G:K.112 Water bridges: G:A.109 CDL.12: 23 residues within 4Å: Chain H: L.97, F.101, F.105 Chain I: T.21, I.24, F.25, I.28, K.32, L.97, F.101, L.104, F.105, I.108 Chain J: T.21, I.24, F.25, I.28, K.32, L.97, F.101, L.104, F.105, I.108 23 PLIP interactions: 3 interactions with chain H, 11 interactions with chain J, 9 interactions with chain I Hydrophobic interactions: H:L.97, H:F.101, H:F.101, J:I.24, J:F.25, J:F.25, J:I.28, J:L.97, J:F.101, J:F.101, J:F.105, I:I.24, I:I.28, I:L.97, I:F.101, I:F.101, I:F.101, I:F.105, I:F.105 Water bridges: J:K.32 Salt bridges: J:K.32, J:K.32, I:K.32

9 x NA: SODIUM ION(Non-functional Binders)

NA.2: 6 residues within 4Å: Chain A: L.61, P.62, T.64, Q.65, Q.110, E.139 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:P.62, A:T.64, A:Q.65, A:Q.65, A:Q.110 NA.3: 7 residues within 4Å: Chain B: L.61, P.62, G.63, T.64, Q.65, Q.110, E.139 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.61, B:T.64, B:Q.65, B:Q.110 NA.4: 6 residues within 4Å: Chain D: L.61, P.62, T.64, Q.65, Q.110, E.139 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.64, D:Q.65, D:Q.65, D:Q.65, D:Q.110 NA.6: 6 residues within 4Å: Chain E: L.61, P.62, T.64, Q.65, Q.110, E.139 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:T.64, E:Q.65, E:Q.65, E:Q.110, E:E.139 NA.7: 6 residues within 4Å: Chain F: L.61, P.62, T.64, Q.65, Q.110, E.139 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:T.64, F:Q.65, F:Q.110, F:E.139 NA.9: 6 residues within 4Å: Chain G: L.61, P.62, T.64, Q.65, Q.110, E.139 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:T.64, G:Q.65, G:Q.110, G:Q.110 NA.11: 7 residues within 4Å: Chain H: L.61, P.62, G.63, T.64, Q.65, Q.110, E.139 5 PLIP interactions: 5 interactions with chain H Hydrogen bonds: H:T.64, H:Q.65, H:Q.65, H:Q.110, H:Q.110 NA.13: 6 residues within 4Å: Chain I: L.61, P.62, T.64, Q.65, Q.110, E.139 4 PLIP interactions: 4 interactions with chain I Hydrogen bonds: I:T.64, I:Q.65, I:Q.110, I:E.139 NA.14: 7 residues within 4Å: Chain J: L.61, P.62, G.63, T.64, Q.65, Q.110, E.139 5 PLIP interactions: 5 interactions with chain J Hydrogen bonds: J:T.64, J:Q.65, J:Q.65, J:Q.110, J:E.139

1 x W3K: N,N-dimethyl-4-(5-methyl-1H-benzimidazol-2-yl)aniline(Non-covalent)

W3K.15: 13 residues within 4Å: Chain B: Y.68, E.139, T.140, I.143 Chain K: L.577, I.584, F.588, L.611, L.614, N.615, L.618, T.619, S.622 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain K Hydrophobic interactions: B:T.140, B:I.143, K:F.588, K:N.615, K:L.618, K:L.618 Hydrogen bonds: B:T.140

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Suzuki, K. et al., Novel Inhibitor of Na+-Transporting V-ATPase Suppresses VRE Colonization in Mice and Reveals the High-Resolution Structure of the Na+ Transport Pathway. To Be Published

Release Date

2024-10-09

Peptides

V-type sodium ATPase subunit K: ABCDEFGHIJ
V-type sodium ATPase subunit I: K

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

J
J

K
P

Membrane

We predict this structure to be a membrane protein.
Show / Hide

V-type sodium ATPase subunit K

V-type sodium ATPase subunit I

Related Entries With Identical Sequence