SMTL ID : 8ucl.1

Komagataella pastoris Cytochrome c oxidase in complex with human VMAT2 and Tetrabenazine

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x EBZ: (3S,5R,11bS)-9,10-dimethoxy-3-(2-methylpropyl)-1,3,4,6,7,11b-hexahydro-2H-pyrido[2,1-a]isoquinolin-2-one(Non-covalent)

EBZ.1: 15 residues within 4Å: Chain A: L.37, V.41, F.135, R.189, L.228, V.232, I.308, E.312, F.334, A.337, S.338, Y.341, G.392, I.395, Y.433 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.37, A:F.135, A:Y.341, A:Y.341, A:I.395, A:Y.433

1 x CU: COPPER (II) ION(Non-covalent)

CU.2: 4 residues within 4Å: Chain B: H.243, H.292, H.293 Ligands: HEA.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.243, B:H.292, B:H.293

2 x HEA: HEME-A(Non-covalent)

HEA.3: 18 residues within 4Å: Chain B: G.28, S.35, L.38, R.39, L.42, H.64, A.65, M.68, V.69, L.72, W.129, F.379, H.380, L.383, T.426, F.427, R.440, R.441 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:L.38, B:A.65, B:M.68, B:V.69, B:L.72, B:L.383 Hydrogen bonds: B:R.39, B:W.129, B:Y.373, B:R.441 Salt bridges: B:R.440, B:R.441 HEA.4: 26 residues within 4Å: Chain B: W.129, W.239, H.243, V.246, Y.247, H.292, H.293, I.314, A.315, G.319, G.354, L.355, G.357, V.358, L.360, S.361, D.366, H.370, V.375, H.378, F.379, V.382, L.383, R.440 Chain C: I.35 Ligands: CU.2 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain C, Hydrophobic interactions: B:V.246, B:Y.247, B:A.315, B:L.355, B:V.375, B:F.379, B:F.379, B:V.382, B:L.383, C:I.35, C:I.35 Hydrogen bonds: B:Y.247, B:Y.247 Salt bridges: B:H.370, B:R.440 pi-Cation interactions: B:H.292

1 x CUA: DINUCLEAR COPPER ION(Non-covalent)

CUA.5: 7 residues within 4Å: Chain C: Q.108, H.171, C.206, E.208, C.210, H.214, M.217 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.171, C:C.206, C:C.210, C:C.210

4 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.6: 10 residues within 4Å: Chain B: F.270 Chain C: F.38, I.42, Y.59, M.60, I.66, V.69 Chain J: K.10, I.13, L.14 7 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B, 3 interactions with chain J Hydrophobic interactions: C:F.38, C:I.42, B:F.270, J:I.13, J:L.14 Hydrogen bonds: C:Y.59 Salt bridges: J:K.10 PTY.7: 11 residues within 4Å: Chain B: F.97, A.98, R.99, I.103, I.158 Chain D: H.15, I.62, W.65, H.79, F.94 Ligands: PTY.8 11 PLIP interactions: 6 interactions with chain D, 5 interactions with chain B Hydrophobic interactions: D:I.62, D:W.65, D:W.65, D:F.94, D:F.94, B:I.103, B:I.158 Hydrogen bonds: D:H.15, B:A.98, B:R.99 Salt bridges: B:R.99 PTY.8: 12 residues within 4Å: Chain D: V.70, T.74, L.87, M.218, R.229, H.234, F.235, H.239, H.240, L.241, G.242 Ligands: PTY.7 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:L.241 Hydrogen bonds: D:T.74, D:R.229, D:H.239, D:L.241, D:G.242 Salt bridges: D:R.229 PTY.10: 7 residues within 4Å: Chain B: Y.336, L.341, W.417 Chain F: H.60, K.65, F.69, T.72 6 PLIP interactions: 5 interactions with chain F, 1 interactions with chain B Hydrophobic interactions: F:F.69, B:L.341 Hydrogen bonds: F:H.60, F:H.60 Salt bridges: F:H.60, F:K.65

1 x ZN: ZINC ION(Non-covalent)

ZN.9: 4 residues within 4Å: Chain E: C.82, H.90, C.105, C.108 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.82, E:H.90, E:C.105, E:C.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ye, J. et al., Komagataella pastoris Cytochrome c oxidase in complex with human VMAT2 and Tetrabenazine. To Be Published

Release Date

2024-10-09

Peptides

Synaptic vesicular amine transporter: A
Cytochrome c oxidase subunit 1: B
Cytochrome c oxidase subunit 2: C
Cytochrome c oxidase subunit 3: D
Cytochrome c oxidase subunit 4: E
Cytochrome c oxidase subunit 5: F
Cytochrome c oxidase subunit 6: G
Cytochrome c oxidase subunit 7: H
Cytochrome c oxidase subunit 8: I
Cytochrome c oxidase subunit 9: J

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
a

C
b

D
c

E
d

F
e

G
f

H
g

I
h

J
i

Membrane

We predict this structure to be a membrane protein.
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Synaptic vesicular amine transporter

Cytochrome c oxidase subunit 1

Cytochrome c oxidase subunit 2

Cytochrome c oxidase subunit 3

Cytochrome c oxidase subunit 4

Cytochrome c oxidase subunit 5

Cytochrome c oxidase subunit 6

Cytochrome c oxidase subunit 7

Cytochrome c oxidase subunit 8

Cytochrome c oxidase subunit 9

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