SMTL ID : 6ymy.1

Cytochrome c oxidase from Saccharomyces cerevisiae

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

CU.1: 4 residues within 4Å: Chain A: H.237, H.286, H.287 Ligands: HEA.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.237, A:H.286, A:H.287

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

HEA.2: 32 residues within 4Å: Chain A: F.15, I.19, G.22, S.29, I.32, R.33, V.55, H.58, A.59, M.62, I.63, V.67, G.122, W.123, Y.367, V.370, F.373, H.374, L.377, S.378, I.382, L.385, F.386, Y.389, I.420, F.421, M.424, R.434, R.435, A.457, L.461, F.464 33 PLIP interactions: 33 interactions with chain A, Hydrophobic interactions: A:I.19, A:V.55, A:A.59, A:I.63, A:I.63, A:V.67, A:Y.367, A:V.370, A:F.373, A:F.373, A:L.377, A:I.382, A:I.382, A:L.385, A:F.386, A:Y.389, A:I.420, A:F.421, A:L.461, A:L.461, A:L.461, A:F.464 Hydrogen bonds: A:R.33, A:W.123, A:Y.367, A:S.378, A:R.435 Salt bridges: A:R.434, A:R.435 pi-Stacking: A:H.58, A:F.421 Metal complexes: A:H.58, A:H.374 HEA.3: 32 residues within 4Å: Chain A: W.123, W.233, V.240, Y.241, I.244, H.286, H.287, I.308, A.309, T.312, G.313, F.317, F.344, T.345, G.348, G.351, V.352, L.354, A.355, D.360, H.364, V.369, H.372, F.373, V.376, L.377, R.434 Chain B: I.35, P.74, I.77, L.78 Ligands: CU.1 26 PLIP interactions: 22 interactions with chain A, 4 interactions with chain B, Hydrophobic interactions: A:V.240, A:V.240, A:I.244, A:T.312, A:F.317, A:F.344, A:T.345, A:V.352, A:L.354, A:V.369, A:F.373, A:F.373, A:V.376, A:L.377, A:L.377, B:I.35, B:P.74, B:I.77, B:L.78 Hydrogen bonds: A:Y.241 Salt bridges: A:H.364, A:R.434 pi-Cation interactions: A:H.237, A:H.237, A:H.286 Metal complexes: A:H.372

7 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)(Non-functional Binders)

PTY.4: 10 residues within 4Å: Chain A: H.324, L.335, I.338, W.411 Chain B: M.42, I.46, M.48 Chain E: S.68, I.71 Ligands: PTY.8 7 PLIP interactions: 2 interactions with chain E, 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: E:I.71, A:L.335, A:I.338, A:W.411, A:W.411, B:I.46 Hydrogen bonds: E:S.68 PTY.5: 18 residues within 4Å: Chain A: F.91, P.92, R.93, I.94, L.156 Chain C: H.14, V.16, L.57, S.61, W.64, F.65, I.68, E.71, H.78, G.89, F.90, F.93 Ligands: PTY.10 12 PLIP interactions: 8 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:L.57, C:W.64, C:W.64, C:F.65, C:F.65, C:F.93, C:F.93, A:L.156 Hydrogen bonds: C:H.14, A:R.93, A:I.94 Salt bridges: A:R.93 PTY.8: 13 residues within 4Å: Chain A: F.264, F.317, L.320, A.321 Chain B: L.38, G.63, T.65, I.66, W.70 Chain I: K.10, V.13, I.14 Ligands: PTY.4 8 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A, 3 interactions with chain I Hydrophobic interactions: B:L.38, B:W.70, A:F.264, A:F.317, A:L.320, I:V.13, I:I.14 Salt bridges: I:K.10 PTY.9: 20 residues within 4Å: Chain A: T.350, F.422, H.425, F.426, I.429 Chain B: T.4, P.5, Y.6, A.7, C.8, Y.9, M.29 Chain I: W.31, F.35, K.39 Chain L: L.26, P.29, G.30, Y.33 Ligands: PTY.15 10 PLIP interactions: 3 interactions with chain I, 4 interactions with chain A, 2 interactions with chain B, 1 interactions with chain L Hydrophobic interactions: I:W.31, I:F.35, A:F.422, A:H.425, A:F.426, A:I.429, B:Y.9, L:P.29 Salt bridges: I:K.39 Hydrogen bonds: B:C.8 PTY.10: 19 residues within 4Å: Chain C: L.58, I.62, F.65, I.68, A.72, T.73, I.86, F.93, M.217, A.220, M.221, R.228, H.233, L.234, H.238, H.239, V.240, G.241 Ligands: PTY.5 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:L.58, C:I.62, C:F.65, C:F.65, C:I.86, C:F.93 Hydrogen bonds: C:T.73, C:V.240, C:G.241 Salt bridges: C:R.228, C:R.228, C:H.238 PTY.13: 2 residues within 4Å: Ligands: PCF.14, PCF.16 No protein-ligand interaction detected (PLIP) PTY.15: 6 residues within 4Å: Chain I: M.27, Y.30, F.35 Chain L: L.26, G.27 Ligands: PTY.9 4 PLIP interactions: 2 interactions with chain L, 2 interactions with chain I Hydrophobic interactions: L:L.26, L:L.26, I:Y.30 Hydrogen bonds: I:Y.30

1 x CN3: (2R,5S,11R,14R)-5,8,11-trihydroxy-2-(nonanoyloxy)-5,11-dioxido-16-oxo-14-[(propanoyloxy)methyl]-4,6,10,12,15-pentaoxa-5,11-diphosphanonadec-1-yl undecanoate(Non-covalent)

CN3.6: 9 residues within 4Å: Chain A: N.402, K.404, L.405, F.462, Y.466, K.483 Chain E: F.70, K.73 Chain H: F.27 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain H Hydrophobic interactions: A:F.462, A:F.462, H:F.27 Hydrogen bonds: A:N.402, A:K.404 Salt bridges: A:K.404, A:K.483

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

CUA.7: 6 residues within 4Å: Chain B: H.171, C.206, E.208, C.210, H.214, M.217 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.171, B:C.206, B:E.208, B:H.214

3 x PCF: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE(Non-covalent)

PCF.11: 20 residues within 4Å: Chain A: S.200, T.204, F.212 Chain C: I.100, Y.188, T.189, A.191, A.192, F.193, T.194, I.195, Y.205, G.209, L.210 Chain K: W.93, T.99, L.100, F.101, W.102, N.107 9 PLIP interactions: 4 interactions with chain K, 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: K:T.99, K:T.99, K:L.100, K:F.101, C:I.195 Hydrophobic interactions: C:I.100, C:L.210, A:T.204, A:F.212 PCF.14: 8 residues within 4Å: Chain A: Y.448 Chain E: V.83, A.87, R.90, M.91, G.94 Ligands: PTY.13, PCF.16 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:Y.448 Hydrophobic interactions: E:V.83, E:V.83 PCF.16: 12 residues within 4Å: Chain A: I.415, V.419, Y.448, I.452 Chain B: Y.6 Chain L: A.31, V.32, F.35, S.36, A.38 Ligands: PTY.13, PCF.14 10 PLIP interactions: 4 interactions with chain A, 5 interactions with chain L, 1 interactions with chain B Hydrophobic interactions: A:I.415, A:I.415, A:V.419, A:I.452, L:A.31, L:V.32, L:F.35 Hydrogen bonds: L:S.36, L:S.36, B:Y.6

1 x ZN: ZINC ION(Non-covalent)

ZN.12: 4 residues within 4Å: Chain D: C.82, H.90, C.105, C.108 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.82, D:H.90, D:C.105

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Berndtsson, J. et al., Respiratory supercomplexes enhance electron transport by decreasing cytochrome c diffusion distance. Embo Rep. (2020)

Release Date

2020-09-09

Peptides

Cytochrome c oxidase subunit 1: A
Cytochrome c oxidase subunit 2: B
Cytochrome c oxidase subunit 3: C
Cytochrome c oxidase subunit 4, mitochondrial: D
Cytochrome c oxidase subunit 5A, mitochondrial: E
Cytochrome c oxidase subunit 6, mitochondrial: F
Cytochrome c oxidase subunit 7, mitochondrial: G
Cytochrome c oxidase subunit 8, mitochondrial: H
Cytochrome c oxidase subunit 9, mitochondrial: I
Cytochrome c oxidase subunit 12, mitochondrial: J
Cytochrome c oxidase subunit 13, mitochondrial: K
Cytochrome c oxidase subunit 26, mitochondrial: L

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
a

B
b

C
c

D
d

E
e

F
f

G
g

H
h

I
i

J
j

K
k

L
m

Membrane

We predict this structure to be a membrane protein.
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Cytochrome c oxidase subunit 1

Cytochrome c oxidase subunit 2

Cytochrome c oxidase subunit 3

Cytochrome c oxidase subunit 4, mitochondrial

Cytochrome c oxidase subunit 5A, mitochondrial

Cytochrome c oxidase subunit 6, mitochondrial

Cytochrome c oxidase subunit 7, mitochondrial

Cytochrome c oxidase subunit 8, mitochondrial

Cytochrome c oxidase subunit 9, mitochondrial

Cytochrome c oxidase subunit 12, mitochondrial

Cytochrome c oxidase subunit 13, mitochondrial

Cytochrome c oxidase subunit 26, mitochondrial

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