SMTL ID : 8ijn.2 (1 other biounit)

Bovine Heart Cytochrome c Oxidase in the Nitric Oxide-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: 35 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, F.377, H.378, L.381, S.382, V.386, M.390, F.393, T.424, F.425, Q.428, R.438, R.439, Y.440, S.461, V.465, M.468 36 PLIP interactions: 36 interactions with chain A, Hydrophobic interactions: A:A.24, A:T.31, A:V.58, A:V.58, A:A.62, A:M.65, A:I.66, A:V.70, A:I.73, A:F.377, A:L.381, A:L.381, A:F.393, A:F.393, A:T.424, A:F.425, A:F.425, A:F.425, A:V.465 Hydrogen bonds: A:S.34, A:S.34, A:R.38, A:Y.54, A:W.126, A:Y.371, 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.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: NO.3 38 PLIP interactions: 32 interactions with chain A, 5 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: A:W.236, 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:F.348, 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.439 Salt bridges: A:H.368, A:R.438, A:R.439 pi-Cation interactions: A:H.240 Metal complexes: A:H.376, NO.3

1 x NO: NITRIC OXIDE(Non-covalent)

NO.3: 7 residues within 4Å: Chain A: H.240, V.243, H.290, H.291, H.376 Ligands: HEA.2, CU.4 No protein-ligand interaction detected (PLIP)

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

CU.4: 4 residues within 4Å: Chain A: H.240, H.290, H.291 Ligands: NO.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.240, A:H.290, A:H.291, NO.3

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 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.11, H2O.12, H2O.13

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

NA.6: 5 residues within 4Å: Chain A: E.40, Q.43, G.45, S.441, D.442 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.442 Water bridges: A:Q.43

3 x TGL: TRISTEAROYLGLYCEROL(Non-covalent)

TGL.7: 24 residues within 4Å: Chain A: F.2, T.17, L.18, L.20, L.21, F.22, W.25, 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 19 PLIP interactions: 10 interactions with chain A, 9 interactions with chain L Hydrophobic interactions: A:T.17, A:L.18, A:L.20, A:L.20, A:F.22, A:W.25, A:W.25, A:W.25, A:L.113, A:I.472, L:I.11, L:F.13, L:F.13, L:F.13, L:F.13, L:F.28, L:F.28, L:F.29, L:F.29 TGL.18: 16 residues within 4Å: Chain A: F.346, V.350, 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, L.39 Chain I: R.43 15 PLIP interactions: 6 interactions with chain B, 1 interactions with chain I, 8 interactions with chain A Hydrophobic interactions: B:V.31, B:F.32, B:L.39, A:F.346, A:F.346, A:V.350, A:F.426, A:F.426, A:H.429, A:F.430, A:F.430 Water bridges: B:G.8, B:F.9 Salt bridges: B:H.24, I:R.43 TGL.31: 21 residues within 4Å: Chain A: W.334, M.339, L.342, G.343, F.414, A.415, F.418 Chain B: L.39, I.42, S.43, L.46, T.47, K.49 Chain D: R.73, S.74, T.75, E.77, W.78, M.86 Chain I: R.16 Ligands: EDO.15 12 PLIP interactions: 2 interactions with chain D, 3 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: D:E.77, B:L.39, B:I.42, B:T.47, A:W.334, A:W.334, A:L.342, A:F.414, A:F.414, A:F.418 Hydrogen bonds: D:W.78 Salt bridges: A:K.411

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: 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 13 PLIP interactions: 3 interactions with chain K, 4 interactions with chain D, 3 interactions with chain M, 3 interactions with chain A Hydrophobic interactions: K:F.9, D:T.80, D:F.87, D:F.87, D:F.87, M:P.12, M:A.16, M:L.19, A:T.408, A:I.412 Water bridges: K:F.9 Salt bridges: K:H.10 Hydrogen bonds: A:T.408 PGV.9: 29 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, M.100, F.148, H.151, L.152 Chain C: H.9, V.11, G.20, A.24, M.27, T.28, N.50, T.53, 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.23 17 PLIP interactions: 10 interactions with chain C, 7 interactions with chain A Hydrophobic interactions: 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.93, A:F.148, A:L.152 Hydrogen bonds: C:W.57, A:R.96, A:R.96, A:M.97 Water bridges: A:A.93 Salt bridges: A:R.96 PGV.24: 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: CDL.26 28 PLIP interactions: 26 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:I.62, C:F.86, 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:T.14, F:E.17 Salt bridges: C:R.221, C:R.221, C:H.231 PGV.25: 10 residues within 4Å: Chain A: D.298 Chain C: T.95, W.99, Y.102, H.103, L.106, A.107 Chain H: N.22, N.24 Ligands: CHD.22 11 PLIP interactions: 5 interactions with chain C, 4 interactions with chain H, 2 interactions with chain A Hydrophobic interactions: C:T.95, C:W.99, C:W.99, C:W.99, C:L.106 Hydrogen bonds: H:N.22 Water bridges: H:N.22, H:Q.23, H:N.24, A:D.298, A:D.298

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

EDO.10: 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.33 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.485, A:V.485 Water bridges: A:V.482, A:C.498 EDO.11: 6 residues within 4Å: Chain A: H.256, T.259, K.265, T.490, N.491 Ligands: EDO.36 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.490, A:T.490, A:N.491 EDO.12: 6 residues within 4Å: Chain A: G.269, Y.270, M.271, G.272 Chain B: E.62 Ligands: CHD.17 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.269, A:M.271, A:G.272 Water bridges: A:Y.270 EDO.13: 4 residues within 4Å: Chain A: K.265, T.489 Chain F: I.70, P.83 No protein-ligand interaction detected (PLIP) EDO.14: 6 residues within 4Å: Chain A: Y.260, Y.261, H.395, P.398, W.494 Chain M: I.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.394, A:H.395 EDO.15: 7 residues within 4Å: Chain A: N.331, I.332, W.334 Chain B: L.46, T.48 Chain D: R.20 Ligands: TGL.31 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.331, A:I.332, B:L.46 Water bridges: B:T.48 EDO.20: 7 residues within 4Å: Chain A: Y.447 Chain B: M.1, A.2, Q.10, L.136, P.166, Y.193 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.2, B:Q.10, B:Y.193, A:Y.447 EDO.21: 2 residues within 4Å: Chain B: L.135, F.206 2 PLIP interactions: 2 interactions with chain B Water bridges: B:T.125, B:T.125 EDO.29: 3 residues within 4Å: Chain C: H.3, H.70 Chain F: L.16 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:H.3, C:H.70 Water bridges: C:Q.4, C:Q.4, C:Q.4, C:Q.4 EDO.30: 4 residues within 4Å: Chain A: P.222 Chain B: G.177 Chain C: E.111 Chain H: W.68 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain B Hydrogen bonds: H:W.68, B:G.177 EDO.32: 8 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.33 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:W.73 EDO.33: 9 residues within 4Å: Chain A: V.485, T.488 Chain D: D.10, Y.11, L.13, P.14, S.15 Ligands: EDO.10, EDO.32 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:L.13 Water bridges: D:S.15 EDO.36: 7 residues within 4Å: Chain A: T.489, T.490 Chain F: S.67, T.68, V.69, W.71 Ligands: EDO.11 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain F Hydrogen bonds: A:T.489, F:S.67, F:V.69 EDO.37: 5 residues within 4Å: Chain A: E.266 Chain F: D.65, N.66, S.67, T.68 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:S.67, F:T.68, F:T.68, F:T.68 Water bridges: F:D.65 EDO.38: 6 residues within 4Å: Chain A: Y.510 Chain F: P.36, K.37, T.39, N.47, L.48 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:L.48

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

4 x CHD: CHOLIC ACID(Non-covalent)

CHD.17: 8 residues within 4Å: Chain A: M.271, G.272, W.275 Chain B: Q.59, E.62, T.63, T.66 Ligands: EDO.12 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:T.66, A:M.271, A:W.275, A:W.275, A:W.275 Hydrogen bonds: B:E.62 CHD.22: 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.25 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:W.288, A:Y.304, A:F.305, C:W.99 Hydrogen bonds: A:T.301, C:W.99 Water bridges: A:D.300, A:T.301 Salt bridges: A:H.233, C:H.103 CHD.27: 5 residues within 4Å: Chain C: R.156, F.164, F.219, L.223 Chain J: F.1 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain J Hydrophobic interactions: 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.42: 6 residues within 4Å: Chain A: I.3 Chain J: Y.32, R.33, M.36, T.37, L.40 5 PLIP interactions: 5 interactions with chain J Hydrophobic interactions: J:Y.32, J:R.33, J:L.40 Hydrogen bonds: J:R.33, J:R.33

4 x DMU: DECYL-BETA-D-MALTOPYRANOSIDE(Non-covalent)(Post Translational Modification)

DMU.19: 10 residues within 4Å: Chain B: H.26, M.29, I.30, L.33, I.34, L.37, I.72, L.75, P.79 Chain I: K.36 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain I Hydrophobic interactions: B:I.30, B:L.33, B:I.34, B:L.37 Hydrogen bonds: B:H.26, I:K.36 Salt bridges: B:H.26 DMU.28: 8 residues within 4Å: Chain C: W.34, M.40, L.43 Chain G: S.61, W.62, G.63, F.69 Ligands: PEK.23 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain G Hydrophobic interactions: C:L.43 Hydrogen bonds: G:S.61, G:G.63 DMU.43: 13 residues within 4Å: Chain A: L.110, L.145 Chain C: S.29, T.32, M.33, F.37 Chain J: Y.45, S.46, Y.48, C.49, L.50, W.52, A.53 9 PLIP interactions: 3 interactions with chain J, 4 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: J:L.50, J:A.53, C:T.32, C:F.37, C:F.37, A:L.110, A:L.145 Hydrogen bonds: J:Y.45, C:F.37 DMU.44: 12 residues within 4Å: Chain A: F.459 Chain D: L.95, W.98, Y.102 Chain L: F.37 Chain M: L.27, L.28, G.31, W.32, L.34, Y.35, H.36 9 PLIP interactions: 3 interactions with chain M, 3 interactions with chain D, 1 interactions with chain L, 2 interactions with chain A Hydrophobic interactions: M:L.27, M:L.34, D:L.95, L:F.37, A:F.459, A:F.459 Hydrogen bonds: M:W.32 Water bridges: D:Y.102, D:Y.102

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.23: 22 residues within 4Å: Chain A: H.151, V.155, L.210, 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.9, DMU.28 18 PLIP interactions: 5 interactions with chain C, 4 interactions with chain A, 9 interactions with chain G Hydrophobic interactions: C:W.34, C:Y.181, C:F.203, C:F.203, A:H.151, A:V.155, A:L.210, A:L.215, G:W.62, G:F.69 Hydrogen bonds: C:I.188, G:T.68, G:F.70, G:F.70, G:N.76, G:N.76 Water bridges: G:F.69, G:F.69 PEK.39: 13 residues within 4Å: Chain C: K.157, H.158, Q.161, T.168, L.169, Y.172 Chain F: A.1 Chain G: R.17, F.21, G.22, L.25, W.36 Ligands: CDL.41 12 PLIP interactions: 5 interactions with chain C, 7 interactions with chain G Hydrophobic interactions: C:L.169, C:Y.172, C:Y.172, G:F.21, G:F.21, G:L.25, G:L.25 Hydrogen bonds: C:K.157, C:K.157, G:R.17 Salt bridges: G:R.17, G:R.17 PEK.40: 5 residues within 4Å: Chain G: S.2, A.3, K.5, G.6, H.8 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:K.5, G:K.5

2 x CDL: CARDIOLIPIN(Non-covalent)

CDL.26: 19 residues within 4Å: Chain C: T.48, M.51, L.52, M.54, Y.55, W.58, R.59, I.62, R.63, F.67, T.213, V.217, F.220, R.221, K.224, H.226 Chain J: K.8, T.27 Ligands: PGV.24 22 PLIP interactions: 20 interactions with chain C, 2 interactions with chain J Hydrophobic interactions: C:T.48, C:Y.55, C:Y.55, C:Y.55, C:Y.55, C:W.58, C:W.58, C:R.59, C:T.213, C:F.220, C:F.220 Hydrogen bonds: C:Y.55, C:R.59 Water bridges: C:Y.55, C:R.59, C:R.59, J:D.28 Salt bridges: C:R.63, C:K.224, C:K.224, C:H.226, J:K.8 CDL.41: 15 residues within 4Å: Chain C: L.127, L.131, T.134, L.138, V.142, V.254 Chain G: L.23, S.27, L.30, C.31, N.34, L.37, H.38, R.42 Ligands: PEK.39 11 PLIP interactions: 4 interactions with chain C, 7 interactions with chain G Hydrophobic interactions: C:L.131, C:L.131, C:T.134, C:L.138, G:L.23, G:L.23, G:L.30, G:L.37 Hydrogen bonds: G:N.34, G:R.42 Salt bridges: G:H.38

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.34: 21 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 Chain E: H.5, E.6, T.7, D.8, F.11, D.40, L.41 Chain I: R.10, A.14, L.17 14 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B, 3 interactions with chain I, 2 interactions with chain E Hydrophobic interactions: A:F.268, A:F.321, A:L.324, A:H.328, B:I.41, B:M.56, B:V.61, I:A.14, I:L.17 Hydrogen bonds: B:D.57 Salt bridges: B:H.52, E:H.5, E:D.8 Water bridges: I:A.14

1 x ZN: ZINC ION(Non-covalent)

ZN.35: 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

2023-04-12

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: 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: 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

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

Cytochrome c oxidase subunit 7B, mitochondrial

Cytochrome c oxidase subunit 7C, mitochondrial

Cytochrome c oxidase subunit 8B, mitochondrial

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