SMTL ID : 6wm4.1

Human V-ATPase in state 3 with SidK and ADP

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-3-3-1-1-3-3-3-1-1-1-1-1-9-1-1-mer

Ligands

8 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.1: 3 residues within 4Å: Chain A: T.486, Y.487, N.488 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.488 NAG.2: 6 residues within 4Å: Chain A: L.494, R.495, G.496 Chain I: N.70, E.71 Chain J: E.87 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain I Hydrogen bonds: A:R.495, A:G.496, I:N.70, I:E.71 NAG.4: 5 residues within 4Å: Chain V: Y.278, F.317, T.319, S.349, N.350 7 PLIP interactions: 7 interactions with chain V Hydrophobic interactions: V:Y.278, V:T.319 Hydrogen bonds: V:Y.278, V:F.317, V:F.317, V:S.349, V:N.350 NAG.5: 3 residues within 4Å: Chain V: N.296, T.298, T.312 1 PLIP interactions: 1 interactions with chain V Hydrogen bonds: V:T.298 NAG.6: 3 residues within 4Å: Chain V: S.259, N.261, P.265 No protein-ligand interaction detected (PLIP) NAG.7: 2 residues within 4Å: Chain V: N.303, F.306 No protein-ligand interaction detected (PLIP) NAG.8: 2 residues within 4Å: Chain V: N.357, R.387 1 PLIP interactions: 1 interactions with chain V Hydrogen bonds: V:R.387 NAG.9: 3 residues within 4Å: Chain V: N.273, S.275, D.284 2 PLIP interactions: 2 interactions with chain V Hydrogen bonds: V:N.273, V:S.275

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

ADP.3: 13 residues within 4Å: Chain M: F.252, G.253, C.254, G.255, K.256, T.257, V.258, F.445, Q.522, N.523, G.524, Y.525 Chain P: R.400 14 PLIP interactions: 12 interactions with chain M, 2 interactions with chain P Hydrogen bonds: M:A.251, M:G.253, M:C.254, M:G.255, M:K.256, M:T.257, M:V.258, M:Q.522, M:G.524 Salt bridges: M:K.256, P:R.400, P:R.400 pi-Stacking: M:F.445, M:Y.525

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, L. et al., Structures of a Complete Human V-ATPase Reveal Mechanisms of Its Assembly. Mol.Cell (2020)

Release Date

2020-11-11

Peptides

V-type proton ATPase 116 kDa subunit a isoform 1: A
V-type proton ATPase subunit C 1: B
V-type proton ATPase subunit E 1: CEG
V-type proton ATPase subunit G 1: DFH
V-type proton ATPase subunit e 1: I
Ribonuclease kappa: J
V-type proton ATPase catalytic subunit A: KLM
V-type proton ATPase subunit B, brain isoform: NOP
SidK: QRS
V-type proton ATPase subunit D: T
V-type proton ATPase subunit F: U
V-type proton ATPase subunit S1: V
Renin receptor: W
V-type proton ATPase 21 kDa proteolipid subunit: X
V-type proton ATPase 16 kDa proteolipid subunit: YZ0123456
V-type proton ATPase subunit d 1: 7
V-type proton ATPase subunit H: 8

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
R

B
O

C
J

E
I

G
H

D
M

F
L

H
K

I
S

J
T

K
B

L
C

M
A

N
E

O
F

P
D

Q
Y

R
Z

S
X

T
G

U
N

V
U

W
V

X
0

Y
1

Z
2

0
3

1
4

2
5

3
6

4
7

5
8

6
9

7
Q

8
P

Membrane

We predict this structure to be a membrane protein.
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V-type proton ATPase 116 kDa subunit a isoform 1

V-type proton ATPase subunit C 1

V-type proton ATPase subunit E 1

V-type proton ATPase subunit G 1

V-type proton ATPase subunit e 1

Ribonuclease kappa

V-type proton ATPase catalytic subunit A

V-type proton ATPase subunit B, brain isoform

SidK

V-type proton ATPase subunit D

V-type proton ATPase subunit F

V-type proton ATPase subunit S1

Renin receptor

V-type proton ATPase 21 kDa proteolipid subunit

V-type proton ATPase 16 kDa proteolipid subunit

V-type proton ATPase subunit d 1

V-type proton ATPase subunit H

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