SMTL ID : 6jy3.1

Monomeric Form of Bovine Heart Cytochrome c Oxidase in the Fully Oxidized State

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 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: 38 residues within 4Å: Chain A: A.24, G.27, M.28, T.31, S.34, I.37, R.38, Y.54, V.58, H.61, A.62, M.65, I.66, M.69, V.70, I.73, G.125, W.126, Y.371, V.374, F.377, H.378, L.381, S.382, V.386, I.389, M.390, F.393, M.417, T.424, F.425, Q.428, R.438, R.439, Y.440, S.458, V.465, M.468 36 PLIP interactions: 36 interactions with chain A, Hydrophobic interactions: A:A.24, 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:I.389, A:F.393, A:F.393, A:T.424, A:V.465 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 Salt bridges: A:R.438, A:R.439 pi-Stacking: A:F.425 Metal complexes: A:H.61, A:H.378 HEA.2: 33 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, 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 38 PLIP interactions: 33 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:I.247, A:T.309, A:T.316, A:V.320, A:T.349, A:L.353, A:I.356, A:I.356, A:L.358, 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.438, A:R.438 Salt bridges: A:H.368, A:R.438, A:R.439 pi-Cation interactions: A:H.240 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.8, H2O.10, H2O.12

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

NA.5: 3 residues within 4Å: Chain A: E.40, G.45, S.441 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.40 NA.17: 3 residues within 4Å: Chain C: H.148, H.232, E.236 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.236

3 x CDL: CARDIOLIPIN(Non-covalent)

CDL.6: 25 residues within 4Å: Chain A: F.2, I.3, W.6, T.17, L.18, L.21, F.22, W.25, W.103, P.106, L.113, F.393, F.400, S.401, I.472 Chain L: I.11, P.12, F.13, S.14, R.20, M.25, F.28, F.29, S.31, A.35 30 PLIP interactions: 17 interactions with chain A, 13 interactions with chain L Hydrophobic interactions: A:F.2, A:F.2, A:W.6, A:T.17, A:L.18, A:L.21, A:F.22, A:W.25, A:W.25, A:W.25, A:W.25, A:W.103, A:P.106, A:L.113, A:F.393, A:F.400, A:I.472, L:I.11, L:F.13, L:F.13, L:F.13, L:F.28, L:F.28, L:F.28, L:F.29, L:F.29, L:A.35 Hydrogen bonds: L:S.14, L:S.14 Salt bridges: L:R.20 CDL.12: 21 residues within 4Å: Chain A: F.346, V.350, N.422, M.423, F.426, H.429, F.430, L.433 Chain B: M.5, L.7, G.8, H.24, L.28, V.31, F.32, S.35, S.36 Chain I: F.31, Y.35, V.39, R.43 17 PLIP interactions: 5 interactions with chain I, 4 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: I:F.31, B:V.31, B:F.32, A:F.346, A:V.350, A:N.422, A:F.426, A:F.426, A:H.429, A:F.430, A:F.430 Water bridges: I:R.43, I:R.43, B:F.9 Salt bridges: I:K.42, I:R.43, B:H.24 CDL.20: 20 residues within 4Å: Chain C: M.51, L.52, M.54, Y.55, W.58, R.59, I.62, R.63, F.67, S.212, T.213, I.216, V.217, F.220, R.221, K.224, H.226 Chain J: K.8, F.12, T.27 22 PLIP interactions: 3 interactions with chain J, 19 interactions with chain C Hydrophobic interactions: J:T.27, C:M.51, C:M.54, C:Y.55, C:Y.55, C:W.58, C:W.58, C:T.213, C:I.216, C:I.216, C:V.217, C:F.220, C:R.221, C:K.224 Salt bridges: J:K.8, J:K.8, C:R.63, C:K.224, C:K.224, C:H.226, C:H.226 Water bridges: C:R.59

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)

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

PGV.8: 33 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, M.100, F.148, H.151, L.152, I.158, L.159, P.200 Chain C: H.9, V.11, G.20, A.24, M.27, T.28, N.50, M.54, W.57, W.58, V.61, E.64, H.71, L.79, G.82, F.86, S.89, E.90, F.93 Ligands: PEK.18, PGV.19, CQX.24 18 PLIP interactions: 9 interactions with chain A, 9 interactions with chain C Hydrophobic interactions: A:F.148, A:L.152, A:I.158, A:L.159, A:P.200, C:A.24, C:T.28, C:W.57, C:W.57, C:W.57, C:W.58, C:F.86, C:F.93 Hydrogen bonds: A:R.96, A:M.97, C:W.57 Water bridges: A:A.93 Salt bridges: A:R.96 PGV.19: 22 residues within 4Å: Chain C: W.58, V.61, I.62, S.65, T.66, H.71, M.83, F.86, E.90, F.93, H.207, I.210, F.214, R.221, H.226, F.227, T.228, H.231, H.232, F.233, G.234 Ligands: PGV.8 26 PLIP interactions: 2 interactions with chain F, 24 interactions with chain C Water bridges: F:Q.12, F:E.17, C:S.65, C:R.221, C:H.231, C:H.231 Hydrophobic interactions: C:W.58, C:W.58, C:W.58, C:W.58, C:W.58, C:W.58, C:I.62, C:F.93, C:I.210, C:I.210, C:F.214, C:F.214, C:F.214 Hydrogen bonds: C:S.65, C:R.221, C:F.233, C:G.234 Salt bridges: C:R.221, C:R.221, C:H.231

8 x CQX: (2S,3S,4S,5S,6R)-2-(2-decoxyethoxy)-6-(hydroxymethyl)oxane-3,4,5-triol(Non-covalent)

CQX.9: 12 residues within 4Å: Chain A: N.406, D.407, T.408, W.409, I.412 Chain D: T.80, A.84, F.87 Chain K: D.8, F.9, H.10 Ligands: CQX.11 15 PLIP interactions: 4 interactions with chain D, 8 interactions with chain A, 3 interactions with chain K Hydrophobic interactions: D:T.80, D:A.84, D:F.87, A:W.409, A:W.409, A:W.409, K:F.9 Water bridges: D:E.77, A:T.408 Hydrogen bonds: A:N.406, A:D.407, A:T.408, A:T.408, K:F.9 Salt bridges: K:H.10 CQX.10: 16 residues within 4Å: Chain A: L.33, G.49, D.50, Q.52, I.53, V.56, A.60, F.109, L.112, L.113, S.116, A.120 Chain L: P.36, I.39, Q.43, L.44 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain L Hydrophobic interactions: A:L.33, A:I.53, A:V.56, A:F.109, A:L.112, A:L.113, L:I.39 Hydrogen bonds: A:D.50, A:D.50 Water bridges: A:L.48 CQX.11: 11 residues within 4Å: Chain A: E.474, S.478, R.480 Chain K: F.9 Chain M: A.6, P.9, T.10, P.12, Q.15, L.19 Ligands: CQX.9 7 PLIP interactions: 3 interactions with chain A, 3 interactions with chain M, 1 interactions with chain K Hydrogen bonds: A:E.474, A:S.478, A:R.480, M:T.10, M:T.10, M:Q.15 Hydrophobic interactions: K:F.9 CQX.14: 11 residues within 4Å: Chain A: F.268, F.321, A.325, H.328 Chain B: I.41, H.52, M.56, E.60, V.61, W.65, L.68 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.41, B:L.68, A:F.321, A:F.321, A:A.325 CQX.15: 4 residues within 4Å: Chain B: H.26, M.29, L.33 Chain I: K.36 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:K.36 Salt bridges: I:K.36 CQX.21: 11 residues within 4Å: Chain C: F.173, Q.177, A.178, Y.181, Y.182, G.205 Chain G: F.69, F.70, H.71 Ligands: CQX.22, CQX.24 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.173, C:Q.177, C:Y.181 CQX.22: 5 residues within 4Å: Chain C: A.178, S.179, Y.182 Chain G: F.70 Ligands: CQX.21 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:A.178 Water bridges: C:L.175, C:S.179 CQX.24: 8 residues within 4Å: Chain C: L.31, W.34, L.47 Chain G: W.62, G.63, F.69 Ligands: PGV.8, CQX.21 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain G Hydrophobic interactions: C:L.31, C:W.34, C:L.47 Hydrogen bonds: G:G.63, G:F.69

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

CUA.13: 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

1 x CHD: CHOLIC ACID(Non-covalent)

CHD.16: 6 residues within 4Å: Chain A: H.233, D.300, T.301, Y.304 Chain C: W.99, H.103 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:W.99, A:T.301 Salt bridges: C:H.103, A:H.233 Hydrophobic interactions: A:Y.304 Water bridges: A:T.301

1 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.18: 24 residues within 4Å: Chain A: H.151, V.155, A.203, T.207, L.210, L.215 Chain C: W.34, F.35, 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 17 PLIP interactions: 5 interactions with chain A, 5 interactions with chain C, 7 interactions with chain G Hydrophobic interactions: A:V.155, A:A.203, A:L.210, A:L.215, A:L.215, C:W.34, C:F.35, C:Y.181, C:F.203, G:F.69 Hydrogen bonds: C:I.188, G:T.68, G:F.70, G:N.76, G:N.76 Water bridges: G:F.69, G:F.69

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

Shinzawa-Itoh, K. et al., Monomeric structure of an active form of bovine cytochromecoxidase. Proc.Natl.Acad.Sci.USA (2019)

Release Date

2019-09-18

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, mitochondrial: 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, mitochondrial: 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, mitochondrial

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, mitochondrial

Cytochrome c oxidase subunit 8B

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