SMTL ID : 2y69.1 (1 other biounit)

Bovine heart cytochrome c oxidase re-refined with molecular oxygen

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 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, 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, S.458, V.465, M.468 40 PLIP interactions: 40 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:F.377, A:F.377, A:L.381, A:L.381, A:V.386, A:V.386, A:F.393, A:F.393, A:T.424, A:F.425, A:V.465 Hydrogen bonds: A:R.38, A:Y.54, 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 Salt bridges: A:R.438, A:R.439 pi-Stacking: A:H.61, A:F.377, A:H.378, A:H.378, A:F.425 Metal complexes: A:H.61, A:H.378 HEA.2: 35 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 Ligands: OXY.4 36 PLIP interactions: 4 interactions with chain B, 32 interactions with chain A, Hydrophobic interactions: B:I.34, B:P.69, B:I.72, B:L.73, A:W.236, A:V.243, A:V.243, A:I.247, A:T.309, A:T.316, A:V.320, A:F.321, A:F.348, A:I.356, A:I.356, A:L.358, A:L.358, A:V.373, A:V.373, A:F.377, A:F.377, A:V.380, A:L.381, A:L.381, A:L.381 Hydrogen bonds: A:Y.244, A:D.364 Water bridges: A:T.127, 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: OXY.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.240, A:H.290, A:H.291

1 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.4: 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)

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.8, H2O.8, H2O.8

3 x CHD: CHOLIC ACID(Non-covalent)

CHD.6: 7 residues within 4Å: Chain A: H.233, W.288, D.300, T.301, Y.304 Chain C: W.99, H.103 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:W.288, A:Y.304, C:W.99 Hydrogen bonds: A:T.301, C:W.99 Water bridges: A:T.301 Salt bridges: A:H.233, C:H.103 CHD.11: 6 residues within 4Å: Chain C: R.156, Q.161, F.164, F.219, L.223 Chain I: F.22 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain I Hydrophobic interactions: C:F.164, C:F.164, C:F.164, C:F.219, C:L.223, I:F.22 Salt bridges: C:R.156 Hydrogen bonds: I:F.22 CHD.14: 11 residues within 4Å: Chain A: M.271, G.272, W.275 Chain B: E.62, T.63, T.66 Chain M: R.26, R.29, F.30, F.33, G.34 9 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A, 4 interactions with chain M Hydrogen bonds: B:E.62 Hydrophobic interactions: A:M.271, A:W.275, A:W.275, A:W.275, M:F.30, M:F.30 Salt bridges: M:R.26, M:R.29

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

CUA.7: 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 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.8: 18 residues within 4Å: Chain A: H.151, V.155, T.207, L.210, L.215 Chain C: W.34, Q.177, A.178, Y.181, Y.182, A.184, F.186, T.187, I.188, F.198, G.202, F.203 Ligands: PGV.9 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:W.34, C:Q.177, C:I.188, C:F.203, A:H.151, A:V.155, A:L.210 Hydrogen bonds: C:Y.181, C:I.188

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

PGV.9: 26 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, M.100, H.151, L.152, V.155 Chain C: H.9, V.11, G.20, A.24, 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 Ligands: PEK.8 16 PLIP interactions: 11 interactions with chain C, 5 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.86, A:L.152 Hydrogen bonds: C:W.57, A:R.96, A:M.97 Water bridges: C:M.83, A:A.93 Salt bridges: A:R.96 PGV.10: 20 residues within 4Å: Chain C: W.58, V.61, I.62, S.65, T.66, H.71, 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 31 PLIP interactions: 29 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:I.210, C:T.213, C:F.214, C:F.214, C:F.214, C:F.214, C:F.214, C:F.233 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.43, F:E.48 Salt bridges: C:R.221, C:R.221, C:H.231

1 x ZN: ZINC ION(Non-covalent)

ZN.12: 4 residues within 4Å: Chain F: C.91, C.93, C.113, C.116 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.91, F:C.93, F:C.113, F:C.116

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

DMU.13: 11 residues within 4Å: Chain D: L.117, W.120, Y.124 Chain K: F.53 Chain L: L.51, L.52, G.55, W.56, L.58, Y.59, H.60 6 PLIP interactions: 1 interactions with chain K, 4 interactions with chain D, 1 interactions with chain L Hydrophobic interactions: K:F.53, D:L.117, D:W.120, D:W.120, D:W.120, L:L.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kaila, V.R.I. et al., A Combined Quantum Chemical and Crystallographic Study on the Oxidized Binuclear Center of Cytochrome C Oxidase. Biochim.Biophys.Acta (2011)

Release Date

2011-02-23

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: D
CYTOCHROME C OXIDASE SUBUNIT 5A: E
CYTOCHROME C OXIDASE SUBUNIT 5B: F
CYTOCHROME C OXIDASE SUBUNIT VIB ISOFORM 1: G
CYTOCHROME C OXIDASE POLYPEPTIDE VIC: H
CYTOCHROME C OXIDASE POLYPEPTIDE 7A1: I
CYTOCHROME C OXIDASE POLYPEPTIDE 7B: J
CYTOCHROME C OXIDASE SUBUNIT 7C: K
CYTOCHROME C OXIDASE POLYPEPTIDE 8H: L
CYTOCHROME C OXIDASE POLYPEPTIDE 6A2: M

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
H

H
I

I
J

J
K

K
L

L
M

M
T

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

CYTOCHROME C OXIDASE SUBUNIT 5A

CYTOCHROME C OXIDASE SUBUNIT 5B

CYTOCHROME C OXIDASE SUBUNIT VIB ISOFORM 1

CYTOCHROME C OXIDASE POLYPEPTIDE VIC

CYTOCHROME C OXIDASE POLYPEPTIDE 7A1

CYTOCHROME C OXIDASE POLYPEPTIDE 7B

CYTOCHROME C OXIDASE SUBUNIT 7C

CYTOCHROME C OXIDASE POLYPEPTIDE 8H

CYTOCHROME C OXIDASE POLYPEPTIDE 6A2

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