SMTL ID : 6wm3.1

Human V-ATPase in state 2 with SidK and ADP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: Y.487, N.488 No protein-ligand interaction detected (PLIP) NAG.2: 7 residues within 4Å: Chain A: L.494, R.495, G.496, P.498 Chain I: N.70, E.71 Chain J: F.90 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.498 Hydrogen bonds: A:R.495, A:R.495 NAG.3: 4 residues within 4Å: Chain K: Y.278, F.317, T.319, N.350 4 PLIP interactions: 4 interactions with chain K Hydrophobic interactions: K:F.317 Hydrogen bonds: K:F.317, K:T.319, K:T.319 NAG.4: 2 residues within 4Å: Chain K: N.296, T.298 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:T.298 NAG.5: 3 residues within 4Å: Chain K: S.259, N.261, P.265 3 PLIP interactions: 3 interactions with chain K Hydrogen bonds: K:S.259, K:S.259, K:S.259 NAG.6: 1 residues within 4Å: Chain K: N.303 No protein-ligand interaction detected (PLIP) NAG.7: 4 residues within 4Å: Chain K: N.357, V.385, A.386, R.387 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:R.387, K:R.387 NAG.8: 2 residues within 4Å: Chain K: N.273, D.284 No protein-ligand interaction detected (PLIP)

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

ADP.9: 14 residues within 4Å: Chain 2: R.400, K.403 Chain Z: A.251, G.253, C.254, G.255, K.256, T.257, V.258, F.445, Q.522, N.523, G.524, Y.525 15 PLIP interactions: 11 interactions with chain Z, 4 interactions with chain 2 Hydrogen bonds: Z:A.251, Z:G.253, Z:C.254, Z:G.255, Z:K.256, Z:T.257, Z:V.258, Z:Q.522, Z:G.524, 2:K.403, 2:K.403 Salt bridges: Z:K.256, 2:R.400, 2:R.400 pi-Stacking: Z:F.445

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 subunit S1: K
Renin receptor: L
V-type proton ATPase 21 kDa proteolipid subunit: M
V-type proton ATPase 16 kDa proteolipid subunit: NOPQRSTUV
V-type proton ATPase subunit d 1: W
V-type proton ATPase catalytic subunit A: XYZ
V-type proton ATPase subunit B, brain isoform: 012
SidK: 345
V-type proton ATPase subunit D: 6
V-type proton ATPase subunit F: 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
U

L
V

M
0

N
1

O
2

P
3

Q
4

R
5

S
6

T
7

U
8

V
9

W
Q

X
C

Y
A

Z
B

0
F

1
D

2
E

3
Z

4
X

5
Y

6
G

7
N

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 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 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 H

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