SMTL ID : 6j8m.1 (1 other biounit)

Low-dose structure of bovine heart cytochrome c oxidase in the fully oxidized state determined using 30 keV X-ray

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

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

Ligands

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

HEA.1: 35 residues within 4Å: Chain A: G.27, M.28, T.31, S.34, I.37, R.38, Y.54, V.58, H.61, A.62, M.65, I.66, V.70, I.73, G.125, W.126, Y.371, V.374, F.377, H.378, L.381, S.382, V.386, F.393, M.417, T.424, F.425, Q.428, R.438, R.439, Y.440, S.458, V.465, M.468, I.472 37 PLIP interactions: 37 interactions with chain A, Hydrophobic interactions: A:I.37, A:R.38, A:V.58, A:V.58, A:A.62, A:M.65, A:I.66, A:V.70, A:V.374, A:F.377, A:F.377, A:L.381, A:L.381, A:V.386, A:V.386, A:F.393, A:F.393, A:T.424, A:I.472 Hydrogen bonds: A:R.38, A:Y.54, A:W.126, A:Y.371, A:S.382, A:Q.428, A:R.439, A:Y.440 Water bridges: A:R.438, A:R.438, A:S.461 Salt bridges: A:R.438, A:R.439 pi-Stacking: A:H.61, A:H.61, A:F.425 Metal complexes: A:H.61, A:H.378 HEA.2: 34 residues within 4Å: Chain A: W.126, W.236, V.243, Y.244, I.247, H.290, H.291, T.309, I.312, A.313, T.316, G.317, V.320, F.348, T.349, G.352, L.353, G.355, I.356, L.358, A.359, D.364, H.368, V.373, H.376, F.377, V.380, L.381, R.438 Chain B: I.34, P.69, I.72, L.73 Ligands: PER.7 35 PLIP interactions: 30 interactions with chain A, 5 interactions with chain B, Hydrophobic interactions: A:W.236, A:V.243, A:V.243, A:V.243, A:I.247, A:T.309, A:T.316, A:V.320, A:F.348, A:I.356, A:I.356, A:L.358, A:V.373, A:V.373, A:F.377, A:F.377, A:V.380, A:L.381, A:L.381, B:I.34, B:I.34, B:P.69, B:I.72, B:L.73 Hydrogen bonds: A:W.126, A:Y.244 Water bridges: A:H.291, A:T.316, A:D.369, A:D.369, A:R.439 Salt bridges: A:H.368, A:R.438, A:R.439 Metal complexes: A:H.376

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

CU.3: 4 residues within 4Å: Chain A: H.240, H.290, H.291 Ligands: PER.7 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.240, A:H.290, A:H.291

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: H.368, D.369 Chain B: S.197, E.198 6 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:H.368, A:D.369, B:E.198, H2O.12, H2O.13, H2O.16

2 x NA: SODIUM ION(Non-functional Binders)

NA.5: 5 residues within 4Å: Chain A: E.40, Q.43, G.45, S.441, D.442 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.441, A:D.442 Water bridges: A:Q.43 NA.12: 4 residues within 4Å: Chain C: H.148, M.152, H.232, E.236 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.236

4 x PGV: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE(Non-covalent)

PGV.6: 14 residues within 4Å: Chain A: N.406, T.408, W.409, I.412 Chain D: T.80, A.84, F.87 Chain K: F.9, H.10 Chain M: P.12, Q.15, A.16, L.19, S.20 15 PLIP interactions: 3 interactions with chain D, 4 interactions with chain K, 3 interactions with chain M, 5 interactions with chain A Hydrophobic interactions: D:T.80, D:A.84, D:F.87, K:F.9, K:F.9, M:P.12, M:Q.15, M:L.19, A:W.409 Hydrogen bonds: K:H.10, A:N.406, A:T.408 Salt bridges: K:H.10 Water bridges: A:D.407, A:R.480 PGV.8: 28 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, M.100, F.148, H.151, V.155, I.158, P.200 Chain C: H.9, V.11, G.20, A.24, T.28, N.50, T.53, M.54, W.57, W.58, V.61, E.64, H.71, L.79, G.82, F.86, E.90 Ligands: PEK.13 17 PLIP interactions: 7 interactions with chain A, 10 interactions with chain C Hydrophobic interactions: A:F.148, A:V.155, A:I.158, A:P.200, C:A.24, C:T.28, C:T.53, C:W.57, C:W.57, C:W.57, C:W.58, C:F.86, C:F.86 Hydrogen bonds: A:R.96, A:M.97 Salt bridges: A:R.96 Water bridges: C:M.83 PGV.15: 24 residues within 4Å: Chain C: L.47, M.51, M.54, W.58, V.61, I.62, S.65, T.66, H.71, F.86, E.90, H.207, I.210, T.213, F.214, R.221, H.226, F.227, T.228, H.231, H.232, F.233, G.234 Ligands: CDL.17 28 PLIP interactions: 26 interactions with chain C, 2 interactions with chain F Hydrophobic interactions: C:L.47, C:W.58, C:W.58, C:W.58, C:W.58, C:W.58, C:I.62, C:F.86, C:I.210, C:I.210, C:T.213, C:F.214, C:F.214, C:F.214, C:F.214 Hydrogen bonds: C:S.65, C:R.221, C:F.233, C:G.234 Water bridges: C:S.65, C:R.221, C:H.231, C:H.231, F:Q.12, F:E.17 Salt bridges: C:R.221, C:R.221, C:H.231 PGV.16: 11 residues within 4Å: Chain A: F.237, D.298 Chain C: V.91, T.95, W.99, Y.102, H.103, A.107 Chain H: N.22, N.24 Ligands: CHD.19 9 PLIP interactions: 2 interactions with chain A, 4 interactions with chain H, 3 interactions with chain C Hydrophobic interactions: A:F.237, C:V.91, C:W.99, C:W.99 Hydrogen bonds: A:D.298, H:N.22 Water bridges: H:N.24, H:N.24, H:N.24

1 x PER: PEROXIDE ION(Non-covalent)

PER.7: 6 residues within 4Å: Chain A: H.240, V.243, H.290, H.291 Ligands: HEA.2, CU.3 No protein-ligand interaction detected (PLIP)

3 x TGL: TRISTEAROYLGLYCEROL(Non-covalent)

TGL.9: 15 residues within 4Å: Chain A: F.346, V.350, Y.379, N.422, F.426, H.429, F.430, L.433 Chain B: L.7, G.8, L.28, F.32, S.35, L.39 Chain I: R.43 16 PLIP interactions: 8 interactions with chain A, 6 interactions with chain B, 2 interactions with chain I Hydrophobic interactions: A:F.346, A:F.346, A:F.426, A:F.426, A:F.426, A:H.429, A:F.430, A:F.430, B:L.7, B:F.32, B:F.32, B:L.39 Water bridges: B:F.9, I:R.43 Salt bridges: B:H.24, I:R.43 TGL.21: 23 residues within 4Å: Chain A: W.334, L.342, G.343, F.346, F.414, A.415, F.418, V.419 Chain B: L.39, I.42, S.43, T.47, K.49 Chain D: R.73, S.74, T.75, E.77, W.78, V.81, M.86, I.89 Chain I: R.16, H.20 15 PLIP interactions: 9 interactions with chain A, 4 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: A:W.334, A:W.334, A:L.342, A:F.346, A:F.414, A:F.418, A:F.418, A:V.419, D:E.77, D:I.89, B:L.39, B:T.47 Salt bridges: A:K.411 Hydrogen bonds: D:W.78 Water bridges: D:T.75 TGL.27: 25 residues within 4Å: Chain A: F.2, T.17, L.18, L.20, L.21, F.22, W.25, F.102, P.106, L.113, F.393, F.400, S.401, I.472 Chain L: N.10, I.11, P.12, F.13, S.14, R.20, M.24, M.25, F.28, F.29, S.31 18 PLIP interactions: 11 interactions with chain A, 7 interactions with chain L Hydrophobic interactions: A:T.17, A:L.18, A:L.20, A:L.21, A:W.25, A:W.25, A:F.102, A:L.113, A:F.393, A:I.472, A:I.472, L:I.11, L:F.13, L:F.28, L:F.28, L:F.28, L:F.29, L:F.29

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

CUA.10: 6 residues within 4Å: Chain B: H.161, C.196, E.198, C.200, H.204, M.207 7 PLIP interactions: 7 interactions with chain B Metal complexes: B:H.161, B:C.196, B:C.196, B:E.198, B:C.200, B:C.200, B:H.204

4 x CHD: CHOLIC ACID(Non-covalent)

CHD.11: 7 residues within 4Å: Chain A: M.271, G.272, W.275 Chain B: Q.59, E.62, T.63, T.66 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:M.271, A:W.275, A:W.275, A:W.275, B:T.66 Hydrogen bonds: B:Q.59, B:E.62, B:T.63 CHD.18: 6 residues within 4Å: Chain C: R.156, Q.161, F.164, F.219, L.223 Chain J: F.1 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain J Hydrophobic interactions: C:F.164, C:F.164, C:F.164, C:F.219, C:L.223, J:F.1 Water bridges: C:Q.161 Salt bridges: C:R.156 Hydrogen bonds: J:F.1 CHD.19: 9 residues within 4Å: Chain A: H.233, W.288, D.300, T.301, Y.304, F.305 Chain C: W.99, H.103 Ligands: PGV.16 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:W.288, A:Y.304, A:Y.304, A:F.305, C:W.99 Hydrogen bonds: A:T.301, C:W.99 Water bridges: A:T.301 Salt bridges: A:H.233, C:H.103 CHD.26: 6 residues within 4Å: Chain A: I.3 Chain J: Y.32, R.33, M.36, T.37, L.40 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain J Hydrophobic interactions: A:I.3, J:R.33, J:M.36 Hydrogen bonds: J:R.33

3 x PEK: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE(Non-covalent)

PEK.13: 22 residues within 4Å: Chain A: H.151, V.155, A.203, T.207, L.215 Chain C: W.34, Y.181, Y.182, A.184, F.186, T.187, I.188, F.198, G.202, F.203 Chain G: W.62, T.68, F.69, F.70, H.71, N.76 Ligands: PGV.8 15 PLIP interactions: 8 interactions with chain G, 3 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: G:F.69, G:F.70, A:V.155, A:A.203, A:T.207, C:W.34, C:F.203, C:F.203 Hydrogen bonds: G:T.68, G:F.70, G:N.76, G:N.76, C:I.188 Water bridges: G:F.69, G:F.69 PEK.14: 14 residues within 4Å: Chain C: K.157, H.158, Q.161, F.164, I.165, T.168, Y.172 Chain F: A.1 Chain G: R.17, F.21, G.22, L.25, P.26 Ligands: CDL.24 13 PLIP interactions: 10 interactions with chain C, 3 interactions with chain G Hydrophobic interactions: C:F.164, C:I.165, C:T.168, C:Y.172, C:Y.172, G:F.21, G:P.26 Hydrogen bonds: C:K.157, C:K.157, C:Q.161, G:R.17 Salt bridges: C:K.157, C:H.158 PEK.25: 6 residues within 4Å: Chain G: S.2, A.3, K.5, G.6, H.8 Ligands: CDL.24 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:A.3, G:K.5 Water bridges: G:H.8

2 x CDL: CARDIOLIPIN(Non-covalent)

CDL.17: 21 residues within 4Å: Chain C: M.51, L.52, M.54, Y.55, W.58, R.59, I.62, R.63, F.67, L.175, I.209, T.213, I.216, V.217, F.220, R.221, K.224, H.226 Chain J: K.8, F.12 Ligands: PGV.15 25 PLIP interactions: 24 interactions with chain C, 1 interactions with chain J Hydrophobic interactions: C:M.51, C:L.52, C:Y.55, C:Y.55, C:Y.55, C:Y.55, C:W.58, C:W.58, C:R.59, C:I.62, C:L.175, C:I.209, C:I.216, C:V.217 Hydrogen bonds: C:Y.55, C:R.63, C:R.63 Water bridges: C:R.59, C:K.224, J:G.24 Salt bridges: C:R.63, C:K.224, C:K.224, C:K.224, C:H.226 CDL.24: 18 residues within 4Å: Chain C: N.125, L.127, L.131, T.134, L.138, V.142, V.254 Chain G: W.16, L.23, A.24, S.27, L.30, C.31, N.34, L.37, H.38 Ligands: PEK.14, PEK.25 13 PLIP interactions: 8 interactions with chain G, 5 interactions with chain C Hydrophobic interactions: G:W.16, G:L.23, G:L.30, G:L.37, C:L.131, C:T.134, C:L.138, C:V.254 Hydrogen bonds: G:N.34, G:H.38, C:N.125 Salt bridges: G:H.38, G:H.38

2 x DMU: DECYL-BETA-D-MALTOPYRANOSIDE(Non-covalent)

DMU.20: 10 residues within 4Å: Chain C: S.29, T.32, M.33, F.37 Chain J: S.46, Y.48, C.49, L.50, W.52, A.53 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain J Hydrophobic interactions: C:T.32, C:M.33, C:F.37, C:F.37, C:F.37, J:L.50, J:A.53 Hydrogen bonds: J:Y.45, J:Y.45 DMU.28: 11 residues within 4Å: Chain A: F.459, L.462 Chain D: W.98, Y.102 Chain M: L.27, L.28, A.30, G.31, W.32, Y.35, H.36 8 PLIP interactions: 2 interactions with chain A, 3 interactions with chain D, 3 interactions with chain M Hydrophobic interactions: A:F.459, A:L.462, D:W.98, D:W.98, M:L.27, M:A.30 Water bridges: D:Y.102, M:H.36

1 x PSC: (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE(Non-covalent)

PSC.22: 17 residues within 4Å: Chain A: F.321, A.325, H.328 Chain B: I.41, M.45, H.52, M.56, D.57, V.61, I.64, W.65, L.68, P.69 Chain E: D.8, F.11, L.41 Chain I: R.10 12 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: B:I.41, B:M.56, B:V.61, B:I.64, B:W.65, B:L.68, B:P.69, A:F.321, A:A.325 Hydrogen bonds: B:D.57 Salt bridges: E:D.8 pi-Cation interactions: E:F.11

1 x ZN: ZINC ION(Non-covalent)

ZN.23: 4 residues within 4Å: Chain F: C.60, C.62, C.82, C.85 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.60, F:C.62, F:C.82, F:C.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ueno, G. et al., Low-dose X-ray structure analysis of cytochrome c oxidase utilizing high-energy X-rays. J.Synchrotron Radiat. (2019)

Release Date

2019-06-26

Peptides

Cytochrome c oxidase subunit 1: A
Cytochrome c oxidase subunit 2: B
Cytochrome c oxidase subunit 3: C
Cytochrome c oxidase subunit 4 isoform 1: D
Cytochrome c oxidase subunit 5A: E
Cytochrome c oxidase subunit 5B: F
Cytochrome c oxidase subunit 6A2: G
Cytochrome c oxidase subunit 6B1: H
Cytochrome c oxidase subunit 6C: I
Cytochrome c oxidase subunit 7A1: J
Cytochrome c oxidase subunit 7B: K
Cytochrome c oxidase subunit 7C: L
Cytochrome c oxidase subunit 8B: M

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
L

M
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 isoform 1

Cytochrome c oxidase subunit 5A

Cytochrome c oxidase subunit 5B

Cytochrome c oxidase subunit 6A2

Cytochrome c oxidase subunit 6B1

Cytochrome c oxidase subunit 6C

Cytochrome c oxidase subunit 7A1

Cytochrome c oxidase subunit 7B

Cytochrome c oxidase subunit 7C

Cytochrome c oxidase subunit 8B

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