SMTL ID : 5xdx.1 (1 other biounit)

Bovine heart cytochrome c oxidase in the reduced state with pH 7.3 at 1.99 angstrom resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 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: 36 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, M.390, F.393, M.417, T.424, F.425, Q.428, R.438, R.439, Y.440, V.465, M.468 37 PLIP interactions: 37 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:V.374, A:F.377, 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: 32 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, L.73 37 PLIP interactions: 33 interactions with chain A, 4 interactions with chain B, 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:L.358, A:V.373, A:F.377, A:F.377, A:V.380, A:V.380, A:L.381, A:L.381, B:I.34, B:I.34, B:P.69, 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 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: 3 residues within 4Å: Chain A: H.240, H.290, H.291 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.10, H2O.11, H2O.15

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

NA.5: 6 residues within 4Å: Chain A: E.40, Q.43, G.45, T.46, S.441, D.442 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.441 Water bridges: A:Q.43 NA.21: 3 residues within 4Å: Chain C: H.147, H.231, E.235 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.235

3 x TGL: TRISTEAROYLGLYCEROL(Non-covalent)

TGL.6: 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, L.39 Chain I: Y.35, R.43 14 PLIP interactions: 5 interactions with chain B, 7 interactions with chain A, 2 interactions with chain I Hydrophobic interactions: B:L.7, B:V.31, B:F.32, A:F.346, A:T.354, A:N.422, A:F.426, A:H.429, A:F.430, A:F.430 Water bridges: B:F.9, I:R.43 Salt bridges: B:H.24, I:R.43 TGL.33: 24 residues within 4Å: Chain A: W.334, M.339, L.342, G.343, K.411, F.414, A.415, F.418, V.419 Chain B: I.42, L.46, T.47, T.48, 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 14 PLIP interactions: 8 interactions with chain A, 5 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: A:W.334, A:W.334, A:K.411, A:F.414, A:F.414, A:F.418, A:V.419, D:E.77, D:V.81, D:I.89, B:K.49 Salt bridges: A:K.411 Hydrogen bonds: D:T.75, D:W.78 TGL.45: 23 residues within 4Å: Chain A: T.17, L.18, L.21, F.22, W.25, W.81, 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 22 PLIP interactions: 10 interactions with chain L, 12 interactions with chain A Hydrophobic interactions: L:I.11, L:P.12, L:F.13, L:F.13, L:F.13, L:F.13, L:F.28, L:F.28, L:F.29, L:F.29, A:T.17, A:L.18, A:L.21, A:F.22, A:W.25, A:W.25, A:W.25, A:W.81, A:L.113, A:F.393, A:F.400, A:I.472

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: 27 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, F.148, V.155, I.158, P.200 Chain C: H.8, V.10, G.19, A.23, M.26, T.27, L.30, N.49, T.52, M.53, W.56, W.57, V.60, E.63, H.70, L.78, G.81 Ligands: PEK.22, PGV.24 15 PLIP interactions: 8 interactions with chain C, 7 interactions with chain A Hydrophobic interactions: C:A.23, C:L.30, C:T.52, C:W.56, C:W.56, C:W.56, C:W.57, A:F.148, A:V.155, A:I.158, A:P.200 Water bridges: C:M.82 Hydrogen bonds: A:R.96, A:M.97 Salt bridges: A:R.96 PGV.24: 26 residues within 4Å: Chain C: M.50, M.53, W.57, V.60, I.61, S.64, T.65, H.70, M.82, F.85, E.89, L.205, H.206, I.209, T.212, F.213, R.220, H.225, F.226, T.227, H.230, H.231, F.232, G.233 Ligands: PGV.7, CDL.26 30 PLIP interactions: 28 interactions with chain C, 2 interactions with chain F Hydrophobic interactions: C:W.57, C:W.57, C:W.57, C:W.57, C:W.57, C:W.57, C:I.61, C:F.85, C:F.85, C:L.205, C:I.209, C:I.209, C:T.212, C:F.213, C:F.213, C:F.213, C:F.213 Hydrogen bonds: C:S.64, C:R.220, C:F.232, C:G.233 Water bridges: C:S.64, C:R.220, C:H.230, C:H.230, F:Q.12, F:E.17 Salt bridges: C:R.220, C:R.220, C:H.230 PGV.25: 9 residues within 4Å: Chain A: W.288 Chain C: V.90, T.94, W.98, H.102, L.105, A.106 Chain H: N.24 Ligands: CHD.20 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:V.90, C:T.94, C:W.98, C:W.98, C:W.98, A:W.288 Salt bridges: C:H.102 PGV.46: 17 residues within 4Å: Chain A: N.406, T.408, W.409, R.480 Chain D: T.80, A.84, F.87 Chain K: F.9, H.10 Chain M: A.3, K.4, P.5, P.12, Q.15, A.16, L.19, S.20 18 PLIP interactions: 3 interactions with chain K, 6 interactions with chain M, 5 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: K:F.9, K:F.9, M:P.12, M:Q.15, M:A.16, M:L.19, A:T.408, A:W.409, A:W.409, A:W.409, D:T.80, D:A.84, D:F.87, D:F.87 Salt bridges: K:H.10 Water bridges: M:A.3, M:A.3 Hydrogen bonds: A:T.408

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

EDO.8: 6 residues within 4Å: Chain A: E.507 Chain C: T.4 Chain F: P.30, N.32, P.50, R.56 Ligand excluded by PLIP EDO.9: 7 residues within 4Å: Chain A: Y.260, Y.261, V.394, H.395, P.398, W.494 Chain M: I.1 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: L.136, A.137 Chain B: Q.103, W.104 Ligand excluded by PLIP EDO.11: 8 residues within 4Å: Chain A: M.390, F.393, V.394, L.405, A.410, H.413, M.468, I.471 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain A: P.182, H.256, T.259, K.265, T.490, N.491 Ligands: EDO.40 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: K.265, T.489 Chain F: I.70, S.84 Ligand excluded by PLIP EDO.14: 7 residues within 4Å: Chain A: L.483, V.485, T.488, W.494, G.497, C.498 Chain D: Y.11 Ligand excluded by PLIP EDO.15: 7 residues within 4Å: Chain A: Y.19, N.80, N.98, S.101, G.160, N.163, F.164 Ligand excluded by PLIP EDO.16: 7 residues within 4Å: Chain A: M.71, P.72, I.75, G.76, L.105, S.157, L.195 Ligand excluded by PLIP EDO.19: 2 residues within 4Å: Chain B: E.157 Ligands: EDO.30 Ligand excluded by PLIP EDO.28: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.29: 2 residues within 4Å: Chain C: M.39 Ligands: DMU.31 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain A: P.222 Chain B: G.177 Chain C: E.110 Chain H: W.68 Ligands: EDO.19 Ligand excluded by PLIP EDO.34: 6 residues within 4Å: Chain D: P.14, D.26 Chain E: W.27, R.30 Ligands: EDO.35, EDO.41 Ligand excluded by PLIP EDO.35: 8 residues within 4Å: Chain D: Y.22, D.26 Chain E: W.27, R.30, K.31, N.34 Chain F: P.83 Ligands: EDO.34 Ligand excluded by PLIP EDO.37: 4 residues within 4Å: Chain E: Y.18, K.21, I.24, E.28 Ligand excluded by PLIP EDO.39: 3 residues within 4Å: Chain C: H.230 Chain F: D.9, E.17 Ligand excluded by PLIP EDO.40: 7 residues within 4Å: Chain A: T.489, T.490 Chain F: S.67, T.68, V.69, W.71 Ligands: EDO.12 Ligand excluded by PLIP EDO.41: 5 residues within 4Å: Chain F: F.72, Q.80, R.81, P.83 Ligands: EDO.34 Ligand excluded by PLIP

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

CUA.17: 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.18: 7 residues within 4Å: Chain A: M.271, G.272, W.275 Chain B: Q.59, E.62, T.63, T.66 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:Q.59, B:E.62 Hydrophobic interactions: A:M.271, A:W.275, A:W.275, A:W.275 CHD.20: 9 residues within 4Å: Chain A: H.233, W.288, M.297, D.300, T.301, Y.304 Chain C: W.98, H.102 Ligands: PGV.25 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:W.98, A:W.288, A:Y.304 Salt bridges: C:H.102, A:H.233 Hydrogen bonds: A:T.301 CHD.27: 5 residues within 4Å: Chain C: R.155, L.159, F.163, L.222 Chain J: F.1 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain J Hydrophobic interactions: C:L.159, C:F.163, C:F.163, C:F.163, C:L.222 Salt bridges: C:R.155 Hydrogen bonds: J:F.1 CHD.44: 7 residues within 4Å: Chain A: I.3, L.7 Chain J: Y.32, R.33, M.36, T.37, L.40 6 PLIP interactions: 5 interactions with chain J, 1 interactions with chain A Hydrophobic interactions: J:Y.32, J:M.36, J:L.40, A:I.3 Hydrogen bonds: J:R.33, 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.22: 26 residues within 4Å: Chain A: H.151, V.155, A.203, T.207, L.210, L.215 Chain C: W.33, F.34, Y.180, Y.181, A.183, F.185, T.186, I.187, F.197, G.201, F.202, G.204, L.205 Chain G: W.62, T.68, F.69, F.70, H.71, N.76 Ligands: PGV.7 15 PLIP interactions: 3 interactions with chain A, 7 interactions with chain G, 5 interactions with chain C Hydrophobic interactions: A:V.155, A:A.203, A:L.210, G:F.69, C:W.33, C:F.34, C:I.187, C:F.202 Hydrogen bonds: G:T.68, G:F.70, G:N.76, G:N.76, C:I.187 Water bridges: G:F.69, G:F.69 PEK.23: 11 residues within 4Å: Chain C: K.156, H.157, Q.160 Chain F: A.1 Chain G: R.17, F.21, G.22, L.23, L.25, V.28 Ligands: CDL.42 9 PLIP interactions: 6 interactions with chain G, 1 interactions with chain F, 2 interactions with chain C Hydrophobic interactions: G:F.21, G:L.23, G:L.25, G:V.28 Hydrogen bonds: G:R.17, F:A.1, C:K.156, C:K.156 Salt bridges: G:R.17 PEK.43: 6 residues within 4Å: Chain G: S.2, K.5, D.7, H.8, T.11 Ligands: CDL.42 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:K.5

2 x CDL: CARDIOLIPIN(Non-covalent)

CDL.26: 23 residues within 4Å: Chain C: M.50, L.51, M.53, Y.54, W.57, R.58, I.61, R.62, F.66, T.173, S.211, T.212, I.215, V.216, F.219, R.220, K.223, H.225 Chain J: K.8, F.12, I.30, L.31 Ligands: PGV.24 24 PLIP interactions: 20 interactions with chain C, 4 interactions with chain J Hydrophobic interactions: C:Y.54, C:Y.54, C:W.57, C:W.57, C:R.58, C:I.61, C:T.173, C:T.212, C:I.215, C:V.216, C:F.219, C:F.219, J:I.30, J:L.31 Hydrogen bonds: C:Y.54, C:R.58 Water bridges: C:R.58, C:R.62, J:D.28 Salt bridges: C:R.62, C:K.223, C:K.223, C:H.225, J:K.8 CDL.42: 15 residues within 4Å: Chain C: N.124, L.126, L.130, T.133, V.141, L.249, V.253 Chain G: L.23, S.27, C.31, N.34, L.37, H.38 Ligands: PEK.23, PEK.43 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain G Hydrophobic interactions: C:L.130, C:L.130, C:V.141, C:L.249, C:L.249, C:V.253 Hydrogen bonds: C:N.124, G:N.34 Salt bridges: G:H.38, G:H.38

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

DMU.31: 10 residues within 4Å: Chain C: M.32, N.37, S.38, T.40, I.44 Chain J: G.41, G.42, Y.45 Ligands: EDO.29, DMU.32 9 PLIP interactions: 4 interactions with chain J, 5 interactions with chain C Hydrophobic interactions: J:Y.45, J:Y.45, J:Y.45, C:I.44 Hydrogen bonds: J:Y.45, C:N.37, C:N.37, C:S.38, C:T.40 DMU.32: 12 residues within 4Å: Chain A: L.110, L.145 Chain C: S.28, F.36 Chain J: Y.45, S.46, Y.48, C.49, L.50, W.52, A.53 Ligands: DMU.31 10 PLIP interactions: 5 interactions with chain J, 2 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: J:L.50, J:W.52, J:A.53, A:L.110, A:L.145, C:F.36, C:F.36 Hydrogen bonds: J:Y.45, J:Y.45, C:F.36 DMU.47: 12 residues within 4Å: Chain A: L.35, F.459 Chain D: L.95, W.98, Y.102 Chain L: F.37 Chain M: L.27, L.28, G.31, W.32, Y.35, H.36 10 PLIP interactions: 4 interactions with chain D, 3 interactions with chain A, 2 interactions with chain M, 1 interactions with chain L Hydrophobic interactions: D:L.95, D:W.98, D:W.98, D:W.98, A:L.35, A:F.459, A:F.459, M:L.27, M:L.27, L:F.37

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.36: 20 residues within 4Å: Chain A: F.268, F.321, H.328 Chain B: L.37, I.41, M.45, H.52, T.55, M.56, D.57, V.61, I.64, W.65 Chain E: E.6, T.7, D.8, F.11 Chain I: R.10, A.14, L.17 11 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A, 1 interactions with chain E, 1 interactions with chain I Hydrophobic interactions: B:I.41, B:I.41, B:M.56, B:I.64, B:W.65, A:F.268, A:F.321, A:F.321, I:A.14 Hydrogen bonds: B:D.57 Salt bridges: E:D.8

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 in the ligand-free reduced state at neutral pH. Acta Crystallogr F Struct Biol Commun (2018)

Release Date

2018-02-07

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 polypeptide VIc: I
Cytochrome c oxidase subunit VIIa-heart: J
Cytochrome c oxidase subunit VIIb: K
Cytochrome c oxidase subunit VIIc: L
Cytochrome c oxidase subunit VIII-heart: 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.
Show / Hide

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 polypeptide VIc

Cytochrome c oxidase subunit VIIa-heart

Cytochrome c oxidase subunit VIIb

Cytochrome c oxidase subunit VIIc

Cytochrome c oxidase subunit VIII-heart

Related Entries With Identical Sequence