SMTL ID : 8uco.1

CryoEM structure of Komagataella pastoris Cytochrome c oxidase (9 subunits) in complex with human VMAT2 and Amphetamine

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x 1WE: (2S)-1-phenylpropan-2-amine(Non-covalent)

1WE.1: 11 residues within 4Å: Chain A: N.34, L.228, V.232, N.305, I.308, A.337, Y.341, G.392, I.395, D.399, Y.433 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.228, A:Y.341, A:Y.341, A:I.395 Hydrogen bonds: A:N.305, A:N.305

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: 20 residues within 4Å: Chain B: F.21, S.35, L.38, R.39, A.61, H.64, A.65, M.68, V.69, W.129, Y.373, F.379, H.380, L.383, V.388, L.391, M.430, R.440, R.441, V.467 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:F.21, B:L.38, B:A.65, B:V.69, B:F.379, B:L.383, B:L.383, B:V.388, B:V.467 Hydrogen bonds: B:R.39, B:W.129, B:R.441 Salt bridges: B:R.440, B:R.441 Metal complexes: B:H.380 HEA.4: 23 residues within 4Å: Chain B: W.129, V.246, Y.247, H.292, H.293, I.314, A.315, G.319, T.351, G.354, G.357, V.358, L.360, S.361, D.366, H.370, H.378, F.379, V.382, L.383 Chain C: I.35, P.74 Ligands: CU.2 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain C, Hydrophobic interactions: B:W.129, B:A.315, B:T.351, B:F.379, B:V.382, B:L.383, C:I.35, C:P.74 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 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:C.206

5 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.6: 4 residues within 4Å: Chain B: F.432 Chain C: W.6, I.8, F.9 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:W.6 Hydrophobic interactions: B:F.432 PTY.7: 13 residues within 4Å: Chain B: F.97, A.98, R.99, L.100, I.158 Chain D: H.15, L.30, I.62, W.65, E.72, L.87, F.94 Ligands: PTY.8 11 PLIP interactions: 6 interactions with chain D, 5 interactions with chain B Hydrophobic interactions: D:L.30, D:I.62, D:W.65, D:W.65, D:F.94, D:F.94, B:L.100, B:I.158 Hydrogen bonds: B:A.98, B:R.99 Salt bridges: B:R.99 PTY.8: 15 residues within 4Å: Chain D: F.63, V.66, V.70, T.74, L.87, M.222, I.225, R.229, H.234, F.235, H.239, H.240, L.241, G.242 Ligands: PTY.7 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:F.63, D:V.66, D:V.66, D:I.225 Hydrogen bonds: D:H.79, D:H.239, D:L.241, D:G.242 Salt bridges: D:R.229, D:R.229, D:H.239 PTY.10: 6 residues within 4Å: Chain B: L.341 Chain C: I.47 Chain F: H.60, K.65, F.69, T.72 7 PLIP interactions: 6 interactions with chain F, 1 interactions with chain B Hydrophobic interactions: F:K.65, F:F.69, B:L.341 Hydrogen bonds: F:H.60 Salt bridges: F:H.60, F:H.60, F:K.65 PTY.11: 11 residues within 4Å: Chain B: F.270 Chain C: F.38, Y.59, M.60, I.66, V.69, W.70, L.73 Chain J: K.10, I.13, L.14 8 PLIP interactions: 3 interactions with chain J, 4 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: J:I.13, J:L.14, C:F.38, C:W.70, C:W.70, C:L.73, B:F.270 Salt bridges: J:K.10

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., cryoEM structure of Komagataella pastoris Cytochrome c oxidase (9 subunits) in complex with human VMAT2 and Amphetamin. 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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