SMTL ID : 3ag2.2 (1 other biounit)

Bovine Heart Cytochrome c Oxidase in the Carbon Monoxide-bound Fully Reduced State at 100 K

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 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: 34 residues within 4Å: Chain A: 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, G.125, W.126, Y.371, V.374, F.377, H.378, L.381, S.382, V.386, I.389, F.393, M.417, T.424, F.425, Q.428, R.438, R.439, Y.440, M.468 Ligands: TGL.55 31 PLIP interactions: 31 interactions with chain A, Hydrophobic interactions: A:A.62, A:M.65, A:I.66, A:V.70, A:V.374, A:F.377, A:L.381, A:L.381, A:I.389, A:F.393, A:T.424, A:F.425, 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, 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: 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: CMO.6 36 PLIP interactions: 31 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:A.313, A:T.316, A:V.320, A:L.353, A:I.356, A:I.356, 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 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: CMO.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.240, A:H.290, A:H.291, CMO.6

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: 1 interactions with chain B, 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:E.198, A:H.368, A:D.369, H2O.10, H2O.11, H2O.12

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

NA.5: 5 residues within 4Å: Chain A: E.40, Q.43, G.45, T.46, S.441 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.40 Water bridges: A:Q.43 NA.24: 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

1 x CMO: CARBON MONOXIDE(Non-functional Binders)

CMO.6: 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.7: 22 residues within 4Å: Chain A: W.334, M.339, L.342, G.343, K.411, F.414, A.415 Chain B: L.39, I.42, S.43, L.46, T.47, T.48, K.49 Chain D: R.73, T.75, E.77, W.78, V.81, M.86, I.89 Chain I: R.16 11 PLIP interactions: 2 interactions with chain B, 6 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: B:L.39, B:T.47, A:W.334, A:W.334, A:W.334, A:L.342, A:F.414, D:W.78 Salt bridges: A:K.411 Hydrogen bonds: D:T.75, D:W.78 TGL.17: 18 residues within 4Å: Chain A: F.346, T.354, Y.379, N.422, F.426, 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: 8 interactions with chain A, 7 interactions with chain B, 1 interactions with chain I Hydrophobic interactions: A:F.346, A:T.354, A:F.426, A:F.426, A:F.426, A:F.426, A:H.429, A:F.430, B:L.7, B:V.31, B:F.32, B:F.32 Water bridges: B:G.8, B:F.9 Salt bridges: B:H.24, I:R.43 TGL.55: 28 residues within 4Å: Chain A: F.2, T.17, L.18, L.20, L.21, F.22, A.24, W.25, P.106, F.109, L.110, L.113, F.393, F.400, I.472 Chain L: N.10, I.11, P.12, F.13, S.14, R.20, M.24, M.25, L.27, F.28, F.29 Ligands: HEA.1, EDO.14 20 PLIP interactions: 13 interactions with chain A, 7 interactions with chain L Hydrophobic interactions: A:L.18, A:L.20, A:F.22, A:A.24, A:W.25, A:W.25, A:W.25, A:W.25, A:F.109, A:F.109, A:L.113, A:F.393, A:F.400, L:I.11, L:F.13, L:F.13, L:M.24, L:L.27, L:F.28, L:F.28

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

PGV.8: 26 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, M.100, H.151, V.155 Chain C: H.9, G.20, A.24, 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.26, PGV.28 13 PLIP interactions: 8 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: C:T.28, C:W.57, C:W.57, C:W.57, C:W.58, C:F.86, C:F.86, C:F.93, A:V.155 Hydrogen bonds: A:R.96, A:M.97 Water bridges: A:A.93 Salt bridges: A:R.96 PGV.23: 10 residues within 4Å: Chain A: D.298 Chain C: V.91, L.92, T.95, W.99, Y.102, H.103, L.106, A.107 Ligands: CHD.25 7 PLIP interactions: 5 interactions with chain C, 1 interactions with chain B, 1 interactions with chain H Hydrophobic interactions: C:V.91, C:L.92, C:T.95, C:W.99, C:W.99 Water bridges: B:R.178, H:N.24 PGV.28: 23 residues within 4Å: Chain C: M.54, W.58, V.61, I.62, S.65, T.66, H.71, M.83, 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: 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:I.62, C:F.86, C:F.86, 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 Salt bridges: C:R.221, C:R.221, C:H.231 PGV.57: 13 residues within 4Å: Chain A: N.406, T.408, W.409, R.480 Chain D: A.84, F.87 Chain K: F.9, H.10 Chain M: P.5, A.6, P.12, Q.15, L.19 10 PLIP interactions: 4 interactions with chain D, 2 interactions with chain A, 2 interactions with chain M, 2 interactions with chain K Hydrophobic interactions: D:A.84, D:F.87, D:F.87, D:F.87, A:T.408, A:W.409, M:L.19, K:F.9 Hydrogen bonds: M:A.6 Salt bridges: K:H.10

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

EDO.9: 6 residues within 4Å: Chain A: H.256, T.259, K.265, T.490, N.491 Ligands: EDO.42 Ligand excluded by PLIP EDO.10: 8 residues within 4Å: Chain A: G.269, Y.270, M.271, G.272 Chain B: A.58, Q.59, E.62 Ligands: CHD.15 Ligand excluded by PLIP EDO.11: 9 residues within 4Å: Chain A: L.483, T.484, V.485, T.488, W.494, G.497, C.498 Chain D: Y.11 Ligands: EDO.38 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain A: Y.260, Y.261, V.394, H.395, V.485, W.494 Chain M: I.1 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: K.265, T.489 Chain F: I.70, P.83, S.84 Ligand excluded by PLIP EDO.14: 2 residues within 4Å: Chain A: F.2 Ligands: TGL.55 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain B: D.88, Q.181 Chain H: P.21, N.22, Q.23 Ligand excluded by PLIP EDO.20: 2 residues within 4Å: Chain B: T.125, F.206 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain B: S.156, E.157, P.176 Ligands: EDO.33 Ligand excluded by PLIP EDO.31: 8 residues within 4Å: Chain C: W.146, S.150, H.158 Chain F: A.1, S.2 Chain G: A.13, R.14, R.17 Ligand excluded by PLIP EDO.32: 3 residues within 4Å: Chain C: T.145, H.148, H.149 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain A: P.222, A.223 Chain B: G.177 Chain C: E.111 Ligands: EDO.21 Ligand excluded by PLIP EDO.37: 9 residues within 4Å: Chain A: L.495 Chain D: Y.11, A.12, L.13, P.14 Chain F: F.72, W.73 Ligands: EDO.38, EDO.47 Ligand excluded by PLIP EDO.38: 7 residues within 4Å: Chain A: T.484, T.488 Chain D: Y.11, L.13, S.15 Ligands: EDO.11, EDO.37 Ligand excluded by PLIP EDO.39: 7 residues within 4Å: Chain D: Y.22, D.26 Chain E: W.27, R.30, K.31, N.34 Chain F: P.83 Ligand excluded by PLIP EDO.40: 3 residues within 4Å: Chain E: D.23, I.24, D.25 Ligand excluded by PLIP EDO.42: 7 residues within 4Å: Chain A: T.489, T.490 Chain F: S.67, T.68, V.69, W.71 Ligands: EDO.9 Ligand excluded by PLIP EDO.43: 3 residues within 4Å: Chain A: Y.270 Chain F: D.65, S.67 Ligand excluded by PLIP EDO.44: 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.45: 6 residues within 4Å: Chain A: E.507 Chain C: T.5 Chain F: P.30, N.32, P.50, R.56 Ligand excluded by PLIP EDO.46: 3 residues within 4Å: Chain F: T.53, K.55, W.73 Ligand excluded by PLIP EDO.47: 4 residues within 4Å: Chain F: F.72, Q.80, R.81 Ligands: EDO.37 Ligand excluded by PLIP EDO.50: 6 residues within 4Å: Chain C: G.120 Chain G: A.46, F.47, I.48, L.53, R.54 Ligand excluded by PLIP EDO.51: 4 residues within 4Å: Chain G: P.49, Y.50, H.51, P.79 Ligand excluded by PLIP EDO.52: 4 residues within 4Å: Chain H: F.81, G.83, K.84, I.85 Ligand excluded by PLIP EDO.53: 4 residues within 4Å: Chain I: Y.54, D.55, E.62 Ligands: EDO.54 Ligand excluded by PLIP EDO.54: 5 residues within 4Å: Chain I: D.49, F.50, N.53, Y.54 Ligands: EDO.53 Ligand excluded by PLIP

5 x CHD: CHOLIC ACID(Non-covalent)

CHD.15: 7 residues within 4Å: Chain A: M.271, G.272, W.275 Chain B: E.62, T.63, T.66 Ligands: EDO.10 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:E.62, B:T.63 Water bridges: B:T.63 Hydrophobic interactions: A:M.271, A:W.275, A:W.275, A:W.275 CHD.25: 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.23 9 PLIP interactions: 3 interactions with chain C, 6 interactions with chain A Hydrophobic interactions: C:W.99, A:W.288, A:Y.304, A:F.305 Hydrogen bonds: C:W.99, A:T.301 Salt bridges: C:H.103, A:H.233 Water bridges: A:T.301 CHD.30: 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.36: 7 residues within 4Å: Chain C: W.116, P.117, V.254, W.258, W.259, G.260, S.261 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:W.258, C:W.259 Hydrogen bonds: C:W.259, C:S.261, C:S.261 Water bridges: C:S.261 CHD.56: 8 residues within 4Å: Chain A: M.117 Chain J: F.55 Chain L: A.35, F.38, I.39, R.41, H.42, L.45 6 PLIP interactions: 4 interactions with chain L, 2 interactions with chain J Hydrophobic interactions: L:I.39, L:H.42, J:F.55, J:F.55 Hydrogen bonds: L:R.41, L:R.41

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.18: 17 residues within 4Å: Chain A: F.321, A.325, H.328 Chain B: I.41, H.52, M.56, D.57, E.60, V.61, I.64, W.65, P.69, I.72 Chain E: D.8, D.40, L.41 Chain I: G.11 13 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A, 1 interactions with chain I, 3 interactions with chain E Hydrophobic interactions: B:I.41, B:M.56, B:W.65, B:W.65, B:P.69, B:I.72, A:F.321, A:A.325 Salt bridges: B:H.52 Hydrogen bonds: I:G.11, E:D.8, E:D.8 Water bridges: E:D.40

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.22: 9 residues within 4Å: Chain C: R.80, I.84, V.91, T.95, F.98, W.240, F.244, V.247, F.251 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:I.84, C:V.91, C:V.91, C:F.98, C:W.240, C:W.240, C:V.247, C:F.251, C:F.251 Salt bridges: C:K.77 PEK.26: 24 residues within 4Å: Chain A: H.151, V.155, A.203, T.207, L.215 Chain C: W.34, T.174, Q.177, 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 16 PLIP interactions: 7 interactions with chain C, 6 interactions with chain G, 3 interactions with chain A Hydrophobic interactions: C:W.34, C:T.174, C:Q.177, C:F.203, C:F.203, G:W.62, G:F.69, A:V.155, A:A.203, A:L.215 Hydrogen bonds: C:Y.181, C:I.188, G:T.68, G:F.70, G:N.76 Water bridges: G:F.69 PEK.27: 12 residues within 4Å: Chain C: K.157, H.158, Q.161, I.165, T.168, Y.172 Chain F: A.1 Chain G: R.17, F.21, G.22, L.25, P.26 12 PLIP interactions: 5 interactions with chain G, 6 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: G:F.21, G:L.25, G:P.26, C:I.165, C:T.168, C:Y.172, C:Y.172 Water bridges: G:R.17 Salt bridges: G:R.17 Hydrogen bonds: C:K.157, C:K.157, F:A.1

2 x CDL: CARDIOLIPIN(Non-covalent)

CDL.29: 20 residues within 4Å: Chain C: M.51, L.52, Y.55, W.58, R.59, I.62, R.63, F.67, V.171, T.174, L.175, T.213, I.216, V.217, F.220, K.224, H.226 Chain J: K.8, L.31, V.34 22 PLIP interactions: 20 interactions with chain C, 2 interactions with chain J Hydrophobic interactions: C:M.51, C:L.52, C:Y.55, C:Y.55, C:W.58, C:W.58, C:V.171, C:T.174, C:L.175, C:I.216, C:I.216, C:V.217, C:F.220, J:V.34 Hydrogen bonds: C:Y.55 Water bridges: C:R.59, C:R.59 Salt bridges: C:R.63, C:K.224, C:K.224, C:H.226, J:K.8 CDL.49: 17 residues within 4Å: Chain C: N.125, L.127, L.131, T.134, S.135, L.138, V.142, Y.253, W.258 Chain G: L.23, S.27, L.30, C.31, L.33, N.34, L.37, H.38 14 PLIP interactions: 6 interactions with chain C, 8 interactions with chain G Hydrophobic interactions: C:T.134, C:L.138, C:V.142, C:Y.253, C:W.258, G:L.23, G:L.30, G:L.30, G:L.33, G:N.34, G:L.37 Hydrogen bonds: C:N.125, G:N.34 Salt bridges: G:H.38

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

DMU.34: 11 residues within 4Å: Chain A: L.110 Chain C: S.29, T.32, M.33, F.37 Chain J: Y.45, S.46, Y.48, C.49, W.52 Ligands: DMU.35 6 PLIP interactions: 1 interactions with chain A, 2 interactions with chain J, 3 interactions with chain C Hydrophobic interactions: A:L.110, C:T.32, C:M.33, C:F.37 Hydrogen bonds: J:Y.45, J:Y.48 DMU.35: 10 residues within 4Å: Chain C: N.38, S.39, T.41, I.45 Chain J: T.37, L.38, G.41, G.42, Y.45 Ligands: DMU.34 10 PLIP interactions: 6 interactions with chain C, 4 interactions with chain J Hydrophobic interactions: C:T.41, C:I.45, J:L.38, J:Y.45, J:Y.45 Hydrogen bonds: C:N.38, C:S.39, C:S.39, C:S.39, J:Y.45 DMU.48: 6 residues within 4Å: Chain C: W.34, M.40 Chain G: S.61, W.62, G.63, F.69 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain C Hydrogen bonds: G:S.61, G:G.63 Hydrophobic interactions: C:W.34 DMU.58: 12 residues within 4Å: Chain A: L.35, F.459, L.462 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: 2 interactions with chain M, 3 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: M:L.34, A:L.35, A:F.459, A:L.462, D:W.98, D:W.98, D:W.98 Hydrogen bonds: M:W.32, D:Y.102 DMU.59: 6 residues within 4Å: Chain L: W.19, L.22, A.23, L.27 Chain M: E.14, I.17 4 PLIP interactions: 1 interactions with chain M, 3 interactions with chain L Hydrogen bonds: M:E.14 Hydrophobic interactions: L:W.19, L:L.22, L:L.27

1 x ZN: ZINC ION(Non-covalent)

ZN.41: 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

Muramoto, K. et al., Bovine cytochrome c oxidase structures enable O2 reduction with minimization of reactive oxygens and provide a proton-pumping gate. Proc.Natl.Acad.Sci.USA (2010)

Release Date

2010-04-28

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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