SMTL ID : 9det.1

Human V-ATPase Vo subcomplex (containing subunit isoform a4) bound to nanobody and inhibitor

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

NAG.1: 6 residues within 4Å: Chain C: N.273, S.275, W.282, D.284, M.396, Q.398 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.273, C:N.273 NAG.2: 3 residues within 4Å: Chain C: N.296, T.298, T.312 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.312 NAG.3: 5 residues within 4Å: Chain C: F.301, N.303, D.304, S.305, F.306 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:D.304 Hydrogen bonds: C:N.303 NAG.4: 4 residues within 4Å: Chain C: N.357, V.385, A.386, R.387 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.387 NAG.5: 6 residues within 4Å: Chain C: S.259, Y.260, N.261, P.265, L.297, E.410 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.259, C:N.261 NAG.19: 9 residues within 4Å: Chain A: N.70, E.71, W.74 Chain B: F.90 Chain P: M.497, E.498, E.499, S.500, L.501 3 PLIP interactions: 2 interactions with chain P, 1 interactions with chain B Hydrogen bonds: P:M.497, P:S.500 Hydrophobic interactions: B:F.90 NAG.21: 13 residues within 4Å: Chain A: L.63, F.64 Chain P: T.534, F.535, S.538, K.542, K.597, S.606, A.609, P.610, S.611 Ligands: WJP.20, NAG.22 6 PLIP interactions: 5 interactions with chain P, 1 interactions with chain A Hydrogen bonds: P:S.538, P:K.597, P:A.609 Salt bridges: P:K.542, P:K.597 Hydrophobic interactions: A:F.64 NAG.22: 6 residues within 4Å: Chain A: L.63, F.64 Chain P: S.606, Q.607 Ligands: WJP.20, NAG.21 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:Q.607

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.6: 8 residues within 4Å: Chain C: F.421 Chain D: Y.303, F.307, L.311, I.315 Chain E: A.14, C.18 Ligands: POV.9 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.421

3 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.7: 35 residues within 4Å: Chain C: G.381, S.423, G.425, I.426, G.429, L.430, S.433 Chain D: F.301, E.302, Y.303, S.304, V.305, N.308, M.309, W.312, I.313, A.316, L.317, A.320 Chain F: Y.10, F.13 Chain G: Y.10, F.13, F.14, M.17, S.20, A.21, V.24, F.25, L.86, F.90, L.93, L.97 Chain H: L.97, L.101 13 PLIP interactions: 5 interactions with chain D, 3 interactions with chain G, 1 interactions with chain F, 1 interactions with chain H, 3 interactions with chain C Hydrophobic interactions: D:W.312, D:A.316, D:L.317, G:F.13, G:A.21, G:F.25, F:F.13, H:L.101 Salt bridges: D:E.302 pi-Cation interactions: D:F.301 Hydrogen bonds: C:S.423, C:G.425, C:I.426 POV.8: 28 residues within 4Å: Chain C: Y.332, V.334, S.335, W.339, T.341, T.362 Chain E: G.32, F.33, F.35, D.36, V.37, A.38 Chain L: F.13 Chain M: Y.10, F.13, F.14, L.93, L.97 Chain N: Y.10, F.13, F.14, M.17, A.21, F.25, L.86, F.90, L.93, L.97 8 PLIP interactions: 3 interactions with chain N, 4 interactions with chain C, 1 interactions with chain M Hydrophobic interactions: N:F.14, N:M.17, M:Y.10 Hydrogen bonds: N:Y.10, C:S.335, C:S.335 pi-Cation interactions: C:Y.332, C:W.339 POV.9: 26 residues within 4Å: Chain C: D.417, A.419, S.420, F.421, F.422 Chain D: Y.299, Y.303, F.307, L.311, W.312, I.315, L.319 Chain E: V.11, V.13, A.14, F.15, A.17, C.18, A.21, V.22, C.25, Y.26, F.29, L.31, R.34 Ligands: CLR.6 9 PLIP interactions: 3 interactions with chain D, 4 interactions with chain C, 2 interactions with chain E Hydrophobic interactions: D:F.307, C:F.421, C:F.421, C:F.422, E:F.15, E:Y.26 pi-Cation interactions: D:Y.299, D:Y.303, C:F.421

9 x 01: Cladoniamide A

01.10: 15 residues within 4Å: Chain F: M.53, K.54, I.56, I.57, V.60, F.128 Chain G: L.133, F.137 Chain P: N.439, E.440, I.441, T.444, I.795, M.796, L.799 6 PLIP interactions: 4 interactions with chain F, 2 interactions with chain P Hydrophobic interactions: F:F.128, F:F.128, P:E.440, P:I.441 Hydrogen bonds: F:K.54, F:I.56 01.11: 9 residues within 4Å: Chain G: M.53, K.54, I.56, I.57, V.60, M.61, F.128 Chain H: L.133, F.137 5 PLIP interactions: 5 interactions with chain G Hydrophobic interactions: G:K.54, G:I.56, G:F.128 Hydrogen bonds: G:K.54, G:I.56 01.12: 8 residues within 4Å: Chain H: M.53, K.54, I.56, I.57, V.60, F.128 Chain I: L.133, F.137 4 PLIP interactions: 4 interactions with chain H Hydrophobic interactions: H:K.54, H:F.128 Hydrogen bonds: H:K.54, H:I.56 01.13: 8 residues within 4Å: Chain I: M.53, K.54, I.56, I.57, V.60, F.128 Chain J: L.133, F.137 7 PLIP interactions: 7 interactions with chain I Hydrophobic interactions: I:K.54, I:K.54, I:K.54, I:F.128 Hydrogen bonds: I:K.54, I:I.56, I:I.56 01.14: 8 residues within 4Å: Chain J: M.53, K.54, I.56, I.57, V.60, F.128 Chain K: L.133, F.137 5 PLIP interactions: 5 interactions with chain J Hydrophobic interactions: J:K.54, J:F.128, J:F.128 Hydrogen bonds: J:K.54, J:I.56 01.15: 8 residues within 4Å: Chain K: M.53, K.54, I.56, I.57, V.60, F.128 Chain L: L.133, F.137 5 PLIP interactions: 5 interactions with chain K Hydrophobic interactions: K:K.54, K:K.54, K:I.56 Hydrogen bonds: K:K.54, K:I.56 01.16: 8 residues within 4Å: Chain L: M.53, K.54, I.56, I.57, V.60, F.128 Chain M: L.133, F.137 4 PLIP interactions: 4 interactions with chain L Hydrophobic interactions: L:F.128 Hydrogen bonds: L:K.54, L:I.56, L:I.56 01.17: 8 residues within 4Å: Chain M: M.53, K.54, I.56, I.57, V.60, F.128 Chain N: L.133, F.137 4 PLIP interactions: 1 interactions with chain N, 3 interactions with chain M Hydrophobic interactions: N:L.133 Hydrogen bonds: M:K.54, M:I.56, M:I.56 01.18: 9 residues within 4Å: Chain E: I.178, F.182 Chain N: M.53, K.54, I.56, I.57, V.60, F.128 Chain P: V.721 5 PLIP interactions: 4 interactions with chain N, 1 interactions with chain P Hydrophobic interactions: N:K.54, N:I.56, P:V.721 Hydrogen bonds: N:K.54, N:I.56

1 x WJP: methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate(Non-covalent)

WJP.20: 27 residues within 4Å: Chain E: I.106, I.109, N.113, L.188, V.191, I.192, I.195 Chain P: S.538, M.541, K.542, V.545, F.587, L.590, I.594, K.597, S.611, I.612, L.613, F.616, I.617, F.620, I.735, T.738, A.739, L.742 Ligands: NAG.21, NAG.22 9 PLIP interactions: 9 interactions with chain P Hydrophobic interactions: P:K.542, P:F.587, P:I.594, P:I.617, P:T.738 Hydrogen bonds: P:I.612, P:L.613 Salt bridges: P:K.542, P:K.597

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oot, R.A. et al., Inhibitor bound Vo subcomplex from human V-ATPase. To Be Published

Release Date

2025-09-10

Peptides

V-type proton ATPase subunit e 1: A
Ribonuclease kappa: B
V-type proton ATPase subunit S1: C
Renin receptor: D
V-type proton ATPase 21 kDa proteolipid subunit: E
V-type proton ATPase 16 kDa proteolipid subunit: FGHIJKLMN
V-type proton ATPase subunit d 1: O
V-type proton ATPase 116 kDa subunit a 4: P
Anti V-ATPase Nanobody 2CAS66: Q

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
e

B
f

C
o

D
p

E
b

F
c

G
g

H
h

I
i

J
j

K
k

L
l

M
m

N
n

O
d

P
a

Q
q

Membrane

We predict this structure to be a membrane protein.
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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 116 kDa subunit a 4

Anti V-ATPase Nanobody 2CAS66

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