SMTL ID : 7tap.1

Cryo-EM structure of archazolid A bound to yeast VO V-ATPase

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-8-1-1-1-mer

Ligands

8 x KJL: Archazolid A(Non-covalent)

KJL.1: 13 residues within 4Å: Chain A: V.64, M.65, G.67, I.68, I.71, Y.72, I.142, E.145, V.146 Chain B: F.190, I.193, L.194, L.197 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.64, A:I.68, A:I.68, A:I.71, A:I.142, A:V.146, B:F.190, B:I.193 Hydrogen bonds: A:E.145, A:E.145 KJL.2: 13 residues within 4Å: Chain A: F.143, V.146, L.147, Y.150 Chain E: I.58, G.61, I.62, I.65, Y.66, I.134, E.137, V.138, L.141 14 PLIP interactions: 9 interactions with chain E, 5 interactions with chain A Hydrophobic interactions: E:I.58, E:I.62, E:I.62, E:I.65, E:I.134, E:V.138, E:L.141, A:F.143, A:F.143, A:V.146 Hydrogen bonds: E:E.137, E:E.137, A:F.143, A:Y.150 KJL.3: 15 residues within 4Å: Chain E: F.135, V.138, L.139, Y.142 Chain G: T.32, V.57, I.58, G.61, I.62, I.65, Y.66, I.134, E.137, V.138, L.141 13 PLIP interactions: 8 interactions with chain G, 5 interactions with chain E Hydrophobic interactions: G:I.58, G:I.62, G:I.65, G:E.137, G:E.137, G:V.138, G:L.141, E:F.135, E:V.138, E:V.138 Hydrogen bonds: G:Y.66, E:F.135, E:Y.142 KJL.4: 14 residues within 4Å: Chain G: F.135, V.138, L.139, Y.142 Chain H: I.58, M.59, G.61, I.62, I.65, Y.66, I.134, E.137, V.138, L.141 8 PLIP interactions: 6 interactions with chain H, 2 interactions with chain G Hydrophobic interactions: H:I.62, H:I.65, H:V.138, H:L.141, G:F.135, G:V.138 Hydrogen bonds: H:Y.66, H:E.137 KJL.5: 13 residues within 4Å: Chain H: F.135, V.138, L.139, Y.142 Chain I: I.58, G.61, I.62, I.65, Y.66, I.134, E.137, V.138, L.141 12 PLIP interactions: 3 interactions with chain H, 9 interactions with chain I Hydrophobic interactions: H:F.135, H:F.135, H:V.138, I:I.58, I:I.62, I:I.62, I:I.65, I:I.134, I:V.138, I:L.141 Hydrogen bonds: I:Y.66, I:E.137 KJL.6: 15 residues within 4Å: Chain I: F.135, V.138, L.139, Y.142 Chain J: T.32, I.58, M.59, G.61, I.62, I.65, Y.66, I.134, E.137, V.138, L.141 10 PLIP interactions: 6 interactions with chain J, 4 interactions with chain I Hydrophobic interactions: J:I.62, J:I.62, J:I.65, J:I.134, J:V.138, I:F.135, I:V.138, I:V.138 Hydrogen bonds: J:Y.66, I:F.135 KJL.7: 15 residues within 4Å: Chain J: F.135, V.138, L.139, Y.142 Chain K: T.32, I.58, G.61, I.62, A.64, I.65, Y.66, I.134, E.137, V.138, L.141 14 PLIP interactions: 10 interactions with chain K, 4 interactions with chain J Hydrophobic interactions: K:I.58, K:I.62, K:I.62, K:I.65, K:I.134, K:V.138, K:L.141, J:F.135, J:F.135, J:V.138 Hydrogen bonds: K:Y.66, K:E.137, K:E.137, J:F.135 KJL.8: 13 residues within 4Å: Chain K: F.135, V.138, L.139, Y.142 Chain L: I.58, M.59, G.61, I.62, I.65, Y.66, E.137, V.138, L.141 11 PLIP interactions: 7 interactions with chain L, 4 interactions with chain K Hydrophobic interactions: L:I.58, L:I.62, L:I.65, L:V.138, L:L.141, K:F.135, K:F.135, K:V.138 Hydrogen bonds: L:E.137, L:E.137, K:F.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Keon, K.A. et al., Cryo-EM of the Yeast V O Complex Reveals Distinct Binding Sites for Macrolide V-ATPase Inhibitors. Acs Chem.Biol. (2022)

Release Date

2022-02-23

Peptides

V-type proton ATPase subunit c': A
V-type proton ATPase subunit c'': B
V0 assembly protein 1: C
V-type proton ATPase subunit e: D
V-type proton ATPase subunit c: EGHIJKLM
Yeast V-ATPase subunit f: F
V-type proton ATPase subunit d: N
V-type proton ATPase subunit a, vacuolar isoform: O

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
C

C
N

D
M

E
E

G
F

H
G

I
H

J
I

K
J

L
K

M
L

F
O

N
B

O
A

Membrane

We predict this structure to be a membrane protein.
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V-type proton ATPase subunit c'

V-type proton ATPase subunit c''

V0 assembly protein 1

V-type proton ATPase subunit e

V-type proton ATPase subunit c

Yeast V-ATPase subunit f

V-type proton ATPase subunit d

V-type proton ATPase subunit a, vacuolar isoform

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