SMTL ID : 5xdq.2 (1 other biounit)

Bovine heart cytochrome c oxidase in the fully oxidized state with pH 7.3 at 1.77 angstrom resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 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: L.20, A.24, G.27, 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, 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 Ligands: EDO.13 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:I.73, 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:F.425 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:F.377, 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.8 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:F.348, A:I.356, A:I.356, A:L.358, 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.8 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.11, H2O.13, H2O.16

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

NA.5: 3 residues within 4Å: Chain A: E.40, G.45, S.441 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.43 Water bridges: A:Q.43 NA.20: 3 residues within 4Å: Chain C: H.148, H.232, E.236 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.236, C:E.236

3 x TGL: TRISTEAROYLGLYCEROL(Non-covalent)

TGL.6: 25 residues within 4Å: Chain A: F.2, T.17, L.18, L.20, L.21, F.22, W.25, W.81, P.106, F.109, L.113, F.393, F.400, S.401, I.472 Chain L: N.10, I.11, P.12, F.13, S.14, M.24, M.25, F.28, F.29, S.31 25 PLIP interactions: 16 interactions with chain A, 9 interactions with chain L Hydrophobic interactions: A:L.18, A:L.20, A:L.20, A:L.21, A:L.21, A:F.22, A:W.25, A:W.25, A:W.25, A:W.25, A:W.81, A:F.109, 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 TGL.15: 19 residues within 4Å: Chain A: F.346, Y.379, F.418, N.422, F.426, P.427, H.429, F.430, L.433 Chain B: L.7, G.8, H.24, L.28, V.31, F.32, S.35, S.36, L.39 Chain I: R.43 16 PLIP interactions: 6 interactions with chain B, 8 interactions with chain A, 2 interactions with chain I Hydrophobic interactions: B:V.31, B:F.32, B:L.39, A:F.346, A:F.418, A:F.426, A:F.426, A:P.427, A:H.429, A:F.430, A:F.430 Water bridges: B:G.8, B:F.9, I:R.43 Salt bridges: B:H.24, I:R.43 TGL.32: 21 residues within 4Å: Chain A: W.334, M.339, L.342, G.343, F.414, A.415, F.418, V.419 Chain B: L.39, I.42, S.43, L.46, T.47, K.49 Chain D: R.73, T.75, E.77, W.78, V.81 Chain I: R.16, H.20 13 PLIP interactions: 8 interactions with chain A, 4 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: A:W.334, A:W.334, A:W.334, A:L.342, A:F.414, A:F.418, A:V.419, D:E.77, D:V.81, B:L.39 Salt bridges: A:K.411 Hydrogen bonds: D:T.75, D:W.78

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

PGV.7: 14 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: F.9, H.10 Chain M: P.12, Q.15, A.16, L.19 17 PLIP interactions: 3 interactions with chain D, 3 interactions with chain K, 7 interactions with chain A, 4 interactions with chain M Hydrophobic interactions: D:T.80, D:F.87, D:F.87, K:F.9, K:F.9, A:T.408, A:W.409, A:W.409, A:I.412, M:P.12, M:Q.15, M:A.16, M:L.19 Water bridges: K:F.9 Hydrogen bonds: A:D.407, A:D.407, A:T.408 PGV.9: 29 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, M.100, F.148, L.152, V.155, I.158, P.200 Chain C: H.9, V.11, G.20, A.24, T.28, L.31, N.50, M.54, W.57, W.58, V.61, E.64, H.71, L.79, G.82, M.83, F.86 Ligands: PEK.21, PGV.22 17 PLIP interactions: 8 interactions with chain C, 9 interactions with chain A Hydrophobic interactions: C:A.24, C:T.28, C:L.31, C:W.57, C:W.57, C:W.57, C:F.86, A:F.148, A:L.152, A:I.158, A:P.200 Water bridges: C:M.83, A:A.93 Hydrogen bonds: A:R.96, A:R.96, A:M.97 Salt bridges: A:R.96 PGV.22: 23 residues within 4Å: Chain C: M.51, M.54, W.58, V.61, I.62, S.65, T.66, H.71, F.86, 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: PGV.9, CDL.23 27 PLIP interactions: 25 interactions with chain C, 2 interactions with chain F 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.86, C:I.210, C:I.210, 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.47: 9 residues within 4Å: Chain A: F.237 Chain C: T.95, W.99, H.103, L.106, A.107 Chain H: N.24, R.27 Ligands: CHD.19 12 PLIP interactions: 7 interactions with chain H, 4 interactions with chain C, 1 interactions with chain A Water bridges: H:N.22, H:N.22, H:N.22, H:N.24, H:N.24, H:N.24, H:R.27 Hydrophobic interactions: C:W.99, C:W.99, C:L.106, A:F.237 Salt bridges: C:H.103

1 x PER: PEROXIDE ION(Non-covalent)

PER.8: 5 residues within 4Å: Chain A: H.240, V.243, H.291 Ligands: HEA.2, CU.3 No protein-ligand interaction detected (PLIP)

25 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.10: 6 residues within 4Å: Chain A: H.256, T.259, K.265, T.490, N.491 Ligands: EDO.39 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: Y.260, Y.261, H.395, P.398, W.494 Chain M: I.1 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: K.265, T.489 Chain F: I.70, P.83, S.84 Ligand excluded by PLIP EDO.13: 8 residues within 4Å: Chain A: V.386, M.390, H.413, M.417, A.464, V.465, M.468 Ligands: HEA.1 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: Y.510 Chain F: P.36, K.37, T.39, N.47, L.48 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain A: Y.447 Chain B: M.1, A.2, Q.10, L.136, P.166, Y.193 Ligand excluded by PLIP EDO.25: 3 residues within 4Å: Chain C: P.73, Q.76, R.80 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain C: Y.172, L.175, L.176 Ligand excluded by PLIP EDO.27: 2 residues within 4Å: Chain C: H.3, Q.4 Ligand excluded by PLIP EDO.28: 2 residues within 4Å: Chain C: M.44, T.48 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain A: P.222 Chain B: G.177 Chain C: E.111 Chain H: W.68 Ligands: EDO.30 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain B: G.177 Chain C: E.111 Chain H: W.68, W.72 Ligands: EDO.29 Ligand excluded by PLIP EDO.33: 7 residues within 4Å: Chain A: L.495 Chain D: A.12, L.13, P.14 Chain F: F.72, W.73 Ligands: EDO.41 Ligand excluded by PLIP EDO.34: 3 residues within 4Å: Chain E: Y.18, K.21, E.28 Ligand excluded by PLIP EDO.35: 4 residues within 4Å: Chain E: R.14, W.15, Y.18 Ligands: EDO.36 Ligand excluded by PLIP EDO.36: 5 residues within 4Å: Chain E: W.15, Y.18, K.31, T.35 Ligands: EDO.35 Ligand excluded by PLIP EDO.37: 3 residues within 4Å: Chain E: R.53, R.56, R.57 Ligand excluded by PLIP EDO.39: 7 residues within 4Å: Chain A: T.489, T.490 Chain F: S.67, T.68, V.69, W.71 Ligands: EDO.10 Ligand excluded by PLIP EDO.40: 3 residues within 4Å: Chain C: H.231 Chain F: D.9, E.17 Ligand excluded by PLIP EDO.41: 5 residues within 4Å: Chain F: F.72, Q.80, R.81, P.83 Ligands: EDO.33 Ligand excluded by PLIP EDO.45: 5 residues within 4Å: Chain G: L.25, V.28, A.29, T.32 Ligands: PEK.43 Ligand excluded by PLIP EDO.46: 4 residues within 4Å: Chain G: L.30, L.33, N.34 Ligands: CDL.44 Ligand excluded by PLIP EDO.49: 3 residues within 4Å: Chain J: Q.9, K.10, Q.13 Ligand excluded by PLIP EDO.50: 5 residues within 4Å: Chain C: N.12, P.13 Chain J: G.17, L.18, P.19 Ligand excluded by PLIP EDO.52: 3 residues within 4Å: Chain C: P.13 Chain L: H.2, Y.3 Ligand excluded by PLIP

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

CUA.16: 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 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.17: 22 residues within 4Å: Chain A: F.268, F.321, L.324, A.325, H.328 Chain B: I.41, M.45, H.52, M.56, D.57, V.61, I.64, W.65, L.68 Chain E: H.5, E.6, T.7, D.8, F.11, L.41 Chain I: R.10, L.17 17 PLIP interactions: 6 interactions with chain A, 1 interactions with chain I, 8 interactions with chain B, 2 interactions with chain E Hydrophobic interactions: A:F.268, A:F.321, A:F.321, A:L.324, A:A.325, A:H.328, I:L.17, B:I.41, B:I.41, B:M.56, B:V.61, B:I.64, B:W.65, B:L.68 Hydrogen bonds: B:D.57 Salt bridges: E:H.5, E:D.8

3 x CHD: CHOLIC ACID(Non-covalent)

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.47 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:W.288, A:Y.304, A:F.305, C:W.99 Hydrogen bonds: A:T.301 Water bridges: A:H.233, A:H.233, A:D.298, A:D.300, A:T.301 Salt bridges: A:H.233, C:H.103 CHD.24: 5 residues within 4Å: Chain C: R.156, F.164, F.219, L.223 Chain J: F.1 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain J Hydrophobic interactions: C:F.164, C:F.164, C:F.164, C:F.219, C:L.223 Salt bridges: C:R.156 Hydrogen bonds: J:F.1 CHD.48: 7 residues within 4Å: Chain A: I.3, L.7 Chain J: Y.32, R.33, M.36, T.37, L.40 4 PLIP interactions: 3 interactions with chain J, 1 interactions with chain A Hydrophobic interactions: J:R.33, J:M.36, A:I.3 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.21: 26 residues within 4Å: Chain A: H.151, V.155, A.203, T.207, L.210, L.215 Chain C: W.34, A.178, Y.181, Y.182, A.184, F.186, T.187, I.188, F.198, G.202, F.203, G.205, I.209 Chain G: W.62, T.68, F.69, F.70, H.71, N.76 Ligands: PGV.9 17 PLIP interactions: 6 interactions with chain C, 7 interactions with chain G, 4 interactions with chain A Hydrophobic interactions: C:W.34, C:Y.181, C:F.203, C:F.203, C:I.209, G:W.62, G:F.69, A:V.155, A:A.203, A:L.210, A:L.215 Hydrogen bonds: C:I.188, G:T.68, G:F.70, G:N.76, G:N.76 Water bridges: G:F.69 PEK.42: 8 residues within 4Å: Chain G: S.2, A.3, K.5, G.6, H.8, T.11, L.23 Ligands: CDL.44 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:A.3, G:L.23 Hydrogen bonds: G:H.8 Salt bridges: G:H.8 PEK.43: 15 residues within 4Å: Chain C: H.158, Q.161, I.165, T.168, L.169, Y.172 Chain F: A.1 Chain G: R.17, F.21, G.22, L.23, P.26, W.36 Ligands: CDL.44, EDO.45 14 PLIP interactions: 6 interactions with chain G, 8 interactions with chain C Hydrophobic interactions: G:F.21, G:F.21, G:L.23, G:W.36, C:I.165, C:I.165, C:L.169, C:Y.172, C:Y.172, C:Y.172 Hydrogen bonds: G:R.17, C:H.158 Salt bridges: G:R.17 Water bridges: C:Q.161

2 x CDL: CARDIOLIPIN(Non-covalent)

CDL.23: 21 residues within 4Å: Chain C: M.51, L.52, Y.55, W.58, R.59, I.62, R.63, F.67, T.174, S.212, T.213, I.216, V.217, F.220, R.221, K.224, H.226 Chain J: K.8, D.28, L.31 Ligands: PGV.22 18 PLIP interactions: 2 interactions with chain J, 16 interactions with chain C Hydrogen bonds: J:D.28, C:Y.55, C:R.59 Salt bridges: J:K.8, C:R.63, C:K.224, C:H.226 Hydrophobic interactions: C:L.52, C:Y.55, C:Y.55, C:W.58, C:W.58, C:R.59, C:T.174, C:I.216, C:V.217, C:F.220 Water bridges: C:R.59 CDL.44: 18 residues within 4Å: Chain C: N.125, L.127, L.131, L.138, V.142, Y.253, V.254 Chain G: W.16, L.23, A.24, S.27, L.30, C.31, N.34, H.38 Ligands: PEK.42, PEK.43, EDO.46 12 PLIP interactions: 8 interactions with chain G, 4 interactions with chain C Hydrophobic interactions: G:W.16, G:L.23, G:L.23, G:L.30, G:L.30, C:L.131, C:L.138, C:Y.253 Hydrogen bonds: G:N.34, C:N.125 Salt bridges: G:H.38, G:H.38

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

DMU.31: 8 residues within 4Å: Chain C: F.37, N.38, S.39, I.45 Chain J: G.41, G.42, Y.45 Ligands: DMU.51 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain J Hydrophobic interactions: C:I.45, J:Y.45 Hydrogen bonds: C:F.37, C:N.38, C:S.39 Water bridges: C:M.40 DMU.51: 14 residues within 4Å: Chain A: L.110, L.145 Chain C: L.25, S.29, M.33, F.37 Chain J: Y.45, S.46, Y.48, C.49, L.50, W.52, A.53 Ligands: DMU.31 9 PLIP interactions: 2 interactions with chain A, 4 interactions with chain J, 3 interactions with chain C Hydrophobic interactions: A:L.110, A:L.145, J:L.50, J:W.52, J:A.53, C:L.25, C:F.37, C:F.37 Hydrogen bonds: J:Y.45 DMU.53: 11 residues within 4Å: Chain A: L.35, F.459 Chain D: W.98, Y.102 Chain M: L.27, L.28, G.31, W.32, L.34, Y.35, H.36 9 PLIP interactions: 5 interactions with chain D, 3 interactions with chain A, 1 interactions with chain M Hydrophobic interactions: D:W.98, D:W.98, D:W.98, A:L.35, A:F.459, A:F.459, M:L.27 Hydrogen bonds: D:Y.102, D:Y.102

1 x ZN: ZINC ION(Non-covalent)

ZN.38: 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

Luo, F. et al., Structure of bovine cytochrome c oxidase crystallized at a neutral pH using a fluorinated detergent. Acta Crystallogr F Struct Biol Commun (2017)

Release Date

2017-07-12

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, mitochondrial: D
Cytochrome c oxidase subunit 5A, mitochondrial: E
Cytochrome c oxidase subunit 5B, mitochondrial: 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, mitochondrial: J
Cytochrome c oxidase subunit 7B, mitochondrial: K
Cytochrome c oxidase subunit 7C, mitochondrial: L
Cytochrome c oxidase subunit 8B, mitochondrial: M

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
N

B
O

C
P

D
Q

E
R

F
S

G
T

H
U

I
V

J
W

K
X

L
Y

M
Z

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, mitochondrial

Cytochrome c oxidase subunit 5A, mitochondrial

Cytochrome c oxidase subunit 5B, mitochondrial

Cytochrome c oxidase subunit 6A2, mitochondrial

Cytochrome c oxidase subunit 6B1

Cytochrome c oxidase subunit 6C

Cytochrome c oxidase subunit 7A1, mitochondrial

Cytochrome c oxidase subunit 7B, mitochondrial

Cytochrome c oxidase subunit 7C, mitochondrial

Cytochrome c oxidase subunit 8B, mitochondrial

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