SMTL ID : 5xdx.2 (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: 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, M.417, T.424, F.425, Q.428, R.438, R.439, Y.440, V.465, M.468 35 PLIP interactions: 35 interactions with chain A, Hydrophobic interactions: A:T.31, A:V.58, A:V.58, A:A.62, A:M.65, A:I.66, A:V.70, 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: 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.321, 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 37 PLIP interactions: 32 interactions with chain A, 5 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.321, A:F.348, A:L.353, 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, 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 Salt bridges: A:H.368, A:R.438, A:R.439 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.8, H2O.9, H2O.10

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:D.442 Water bridges: A:Q.43 NA.23: 4 residues within 4Å: Chain C: H.147, M.151, H.231, E.235 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.147, C:E.235

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

PGV.6: 15 residues within 4Å: Chain A: N.406, T.408, W.409, I.412 Chain D: T.80, A.84, F.87 Chain K: D.8, F.9 Chain M: T.10, P.12, Q.15, A.16, L.19, S.20 16 PLIP interactions: 4 interactions with chain A, 4 interactions with chain M, 3 interactions with chain K, 5 interactions with chain D Hydrophobic interactions: A:T.408, A:W.409, A:W.409, A:I.412, M:P.12, M:A.16, M:L.19, K:F.9, K:F.9, D:T.80, D:F.87, D:F.87, D:F.87, D:F.87 Water bridges: M:Q.15 Hydrogen bonds: K:F.9 PGV.7: 30 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, F.148, H.151, V.155, P.200 Chain C: H.8, V.10, G.19, A.23, M.26, T.27, N.49, T.52, M.53, W.56, W.57, V.60, E.63, H.70, L.78, G.81, M.82, F.85, S.88, F.92 Ligands: PGV.24, PEK.37 15 PLIP interactions: 9 interactions with chain C, 6 interactions with chain A Hydrophobic interactions: C:A.23, C:T.27, C:T.52, C:W.56, C:W.56, C:W.56, C:W.57, C:F.85, C:F.92, A:F.148, A:P.200 Hydrogen bonds: A:R.96, A:R.96, A:M.97 Salt bridges: A:R.96 PGV.24: 22 residues within 4Å: Chain C: W.57, V.60, I.61, S.64, T.65, H.70, F.85, H.206, I.208, 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 26 PLIP interactions: 24 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:I.61, C:F.85, C:F.85, C:I.208, C:I.209, 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: 10 residues within 4Å: Chain A: F.237, W.288, D.298 Chain C: T.94, W.98, Y.101, H.102, A.106 Chain H: N.22 Ligands: CHD.22 11 PLIP interactions: 3 interactions with chain A, 5 interactions with chain C, 3 interactions with chain H Hydrophobic interactions: A:F.237, A:W.288, C:T.94, C:W.98, C:W.98, C:W.98 Hydrogen bonds: A:D.298, H:N.22 Salt bridges: C:H.102 Water bridges: H:N.22, H:N.24

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

EDO.8: 6 residues within 4Å: Chain A: Y.260, Y.261, H.395, P.398, W.494 Chain M: I.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.260, A:Y.260, A:V.394, A:H.395 EDO.9: 6 residues within 4Å: Chain A: E.507 Chain C: T.4 Chain F: P.30, N.32, P.50, R.56 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:D.29, F:N.32, A:E.507 EDO.10: 3 residues within 4Å: Chain A: L.136, A.137 Chain B: Q.103 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.103 EDO.11: 7 residues within 4Å: Chain A: L.483, V.485, T.488, W.494, G.497, C.498 Chain D: Y.11 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:L.483, D:Y.11 Water bridges: A:C.498 EDO.12: 8 residues within 4Å: Chain A: P.182, H.256, T.259, K.265, T.490, N.491 Ligands: EDO.13, EDO.34 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.256, A:T.490, A:T.490, A:N.491 EDO.13: 8 residues within 4Å: Chain A: M.86, P.182, H.256, T.490, N.491, E.493 Ligands: EDO.12, EDO.34 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.256, A:N.491 EDO.14: 6 residues within 4Å: Chain A: M.71, P.72, I.75, G.76, L.105, S.157 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.157 EDO.15: 8 residues within 4Å: Chain A: Y.19, N.80, M.92, N.98, S.101, G.160, N.163, F.164 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.19, A:N.80, A:S.101, A:N.163 EDO.16: 5 residues within 4Å: Chain A: K.265, T.489 Chain F: I.70, P.83, S.84 No protein-ligand interaction detected (PLIP) EDO.17: 7 residues within 4Å: Chain A: G.269, M.271, G.272 Chain B: A.58, Q.59, E.62 Ligands: CHD.18 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.269, A:M.271, A:G.272 EDO.28: 6 residues within 4Å: Chain C: F.34, H.35 Chain G: K.58, P.59, F.60, S.61 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain C Hydrogen bonds: G:K.58, G:P.59, C:H.35 EDO.32: 3 residues within 4Å: Chain E: Y.18, K.21, E.28 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:Y.18, E:K.21 Water bridges: E:E.28 EDO.34: 8 residues within 4Å: Chain A: T.489, T.490 Chain F: S.67, T.68, V.69, W.71 Ligands: EDO.12, EDO.13 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:S.67, F:V.69, A:T.489 EDO.35: 5 residues within 4Å: Chain A: E.266 Chain F: D.65, N.66, S.67, T.68 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:D.65, F:S.67, F:T.68, F:T.68, A:E.266

4 x CHD: CHOLIC ACID(Non-covalent)

CHD.18: 7 residues within 4Å: Chain A: M.271, G.272, W.275 Chain B: E.62, T.63, T.66 Ligands: EDO.17 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:E.62, B:T.63 Hydrophobic interactions: A:M.271, A:W.275, A:W.275, A:W.275 CHD.22: 9 residues within 4Å: Chain A: H.233, W.288, D.300, T.301, Y.304, F.305 Chain C: W.98, H.102 Ligands: PGV.25 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:W.288, A:Y.304, A:F.305, C:W.98 Hydrogen bonds: A:T.301 Water bridges: A:H.233 Salt bridges: A:H.233, C:H.102 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.40: 8 residues within 4Å: Chain A: I.3, L.7, F.8 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:R.33, J:M.36, J:L.40, A:I.3 Hydrogen bonds: J:R.33

3 x TGL: TRISTEAROYLGLYCEROL(Non-covalent)

TGL.19: 17 residues within 4Å: Chain A: F.346, V.350, T.354, 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 16 PLIP interactions: 10 interactions with chain A, 5 interactions with chain B, 1 interactions with chain I Hydrophobic interactions: A:F.346, A:F.346, A:V.350, A:V.350, A:T.354, A:N.422, A:F.426, A:F.426, A:H.429, A:F.430, B:L.7, B:V.31, B:F.32, B:L.39 Salt bridges: B:H.24, I:R.43 TGL.31: 18 residues within 4Å: Chain A: W.334, M.339, L.342, G.343, F.346, F.414, A.415 Chain B: L.39, I.42, S.43, T.47, K.49 Chain D: T.75, E.77, W.78, V.81 Chain I: R.16, H.20 12 PLIP interactions: 6 interactions with chain A, 5 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.346, D:E.77, D:W.78, D:V.81, B:L.39 Salt bridges: A:K.411 Hydrogen bonds: D:W.78 Water bridges: D:E.77 TGL.41: 25 residues within 4Å: Chain A: F.2, T.17, L.18, L.20, L.21, F.22, W.25, P.106, F.109, L.110, L.113, F.393, F.400, S.401, I.472 Chain L: N.10, I.11, P.12, F.13, R.20, M.24, M.25, F.28, F.29, S.31 18 PLIP interactions: 10 interactions with chain A, 8 interactions with chain L Hydrophobic interactions: A:T.17, A:L.18, A:L.20, A:L.21, A:F.22, A:W.25, A:W.25, A:F.109, A:L.113, A:F.400, L:I.11, L:F.13, L:F.13, L:F.13, L:F.28, L:F.28, L:F.29, L:F.29

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

CUA.20: 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.21: 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, E.60, V.61, W.65, P.69 Chain E: E.6, T.7, D.8, F.11, L.41 Chain I: R.10, L.17 12 PLIP interactions: 6 interactions with chain A, 5 interactions with chain B, 1 interactions with chain E Hydrophobic interactions: A:F.268, A:F.321, A:F.321, A:L.324, A:A.325, A:H.328, B:I.41, B:I.41, B:V.61, B:P.69 Hydrogen bonds: B:D.57 Salt bridges: E:D.8

2 x CDL: CARDIOLIPIN(Non-covalent)

CDL.26: 21 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, T.212, I.215, V.216, F.219, R.220, K.223, H.225 Chain J: K.8, D.28, L.31 Ligands: PGV.24 17 PLIP interactions: 15 interactions with chain C, 2 interactions with chain J Hydrophobic interactions: C:Y.54, C:W.57, C:W.57, C:R.58, C:T.173, C:T.212, C:I.215, C:I.215 Hydrogen bonds: C:Y.54, C:R.58, J:D.28 Water bridges: C:R.58 Salt bridges: C:R.62, C:K.223, C:K.223, C:H.225, J:K.8 CDL.39: 16 residues within 4Å: Chain C: N.124, L.126, L.130, L.137, V.141, Y.252, V.253 Chain G: L.23, S.27, L.30, C.31, N.34, L.37, H.38 Ligands: PEK.36, PEK.38 14 PLIP interactions: 8 interactions with chain C, 6 interactions with chain G Hydrophobic interactions: C:L.130, C:L.130, C:L.137, C:L.137, C:Y.252, C:V.253, G:L.23, G:L.30, G:L.30 Hydrogen bonds: C:N.124, G:N.34 Water bridges: C:E.127 Salt bridges: G:H.38, G:H.38

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

DMU.29: 7 residues within 4Å: Chain C: F.36, N.37, S.38, I.44 Chain J: G.41, Y.45 Ligands: DMU.30 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:I.44 Hydrogen bonds: C:F.36, C:N.37, C:S.38 Water bridges: C:M.39 DMU.30: 13 residues within 4Å: Chain A: L.110, A.114, L.145 Chain C: S.28, F.36 Chain J: Y.45, S.46, Y.48, C.49, W.52, A.53, H.57 Ligands: DMU.29 8 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A, 3 interactions with chain J Hydrophobic interactions: C:F.36, C:F.36, A:L.110, A:A.114, A:L.145, J:W.52, J:A.53 Hydrogen bonds: J:Y.45 DMU.42: 12 residues within 4Å: Chain A: L.35, F.459 Chain D: L.95, W.98 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 A, 2 interactions with chain M, 1 interactions with chain L, 3 interactions with chain D Hydrophobic interactions: A:L.35, A:F.459, A:F.459, M:L.27, M:L.34, L:F.37, D:L.95, D:W.98, D:W.98

1 x ZN: ZINC ION(Non-covalent)

ZN.33: 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

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.36: 7 residues within 4Å: Chain G: S.2, G.6, H.8, T.11, W.16, L.19 Ligands: CDL.39 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:H.8, G:W.16, G:L.19 PEK.37: 27 residues within 4Å: Chain A: H.151, V.155, A.203, T.207, L.210, L.215 Chain C: W.33, F.34, A.177, Y.180, Y.181, A.183, F.185, T.186, I.187, F.197, G.201, F.202, G.204, I.208 Chain G: W.62, T.68, F.69, F.70, H.71, N.76 Ligands: PGV.7 20 PLIP interactions: 9 interactions with chain C, 4 interactions with chain A, 7 interactions with chain G Hydrophobic interactions: C:W.33, C:F.34, C:Y.180, C:I.187, C:F.202, C:F.202, C:I.208, A:V.155, A:A.203, A:L.210, A:L.215, G:W.62, G:F.69 Hydrogen bonds: C:Y.180, C:I.187, G:T.68, G:F.70, G:N.76 Water bridges: G:F.69, G:F.69 PEK.38: 14 residues within 4Å: Chain C: K.156, H.157, Q.160, I.164, T.167, L.168, Y.171 Chain F: A.1 Chain G: R.17, F.21, L.23, L.25, P.26 Ligands: CDL.39 14 PLIP interactions: 8 interactions with chain C, 6 interactions with chain G Hydrophobic interactions: C:I.164, C:I.164, C:L.168, C:Y.171, C:Y.171, G:F.21, G:F.21, G:L.23, G:L.25 Hydrogen bonds: C:K.156, C:H.157, G:R.17 Water bridges: C:Q.160 Salt bridges: G:R.17

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
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.
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