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

Bovine heart cytochrome c oxidase re-refined with molecular oxygen

Coordinates

PDB Format Compare

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

3 x CHD: CHOLIC ACID(Non-covalent)

CHD.1: 11 residues within 4Å: Chain A: R.26, R.29, F.30, F.33, G.34 Chain B: M.271, G.272, W.275 Chain C: E.62, T.63, T.66 13 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: A:F.30, A:F.30, B:M.271, B:W.275, B:W.275, B:W.275 Water bridges: A:R.29, A:R.29, C:T.63 Salt bridges: A:R.26, A:R.29 Hydrogen bonds: C:E.62, C:T.63 CHD.7: 7 residues within 4Å: Chain B: H.233, W.288, D.300, T.301, Y.304 Chain D: W.99, H.103 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: B:W.288, B:T.301, B:Y.304, D:W.99 Hydrogen bonds: B:T.301, D:W.99 Salt bridges: B:H.233, D:H.103 CHD.12: 5 residues within 4Å: Chain D: R.156, F.164, F.219, L.223 Chain J: F.22 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain J Hydrophobic interactions: D:F.164, D:F.164, D:F.219, D:L.223, J:F.22 Salt bridges: D:R.156 Hydrogen bonds: J:F.22

2 x HEA: HEME-A(Non-covalent)

HEA.2: 35 residues within 4Å: Chain B: 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.458, V.465, M.468 37 PLIP interactions: 37 interactions with chain B, Hydrophobic interactions: B:A.24, B:I.37, B:R.38, B:V.58, B:V.58, B:A.62, B:M.65, B:I.66, B:V.70, B:I.73, B:F.377, B:L.381, B:L.381, B:F.393, B:F.393, B:T.424, B:V.465 Hydrogen bonds: B:R.38, B:Y.54, B:Y.54, B:W.126, B:Y.371, B:S.382, B:Q.428, B:R.439, B:Y.440 Water bridges: B:S.461 Salt bridges: B:R.438, B:R.439 pi-Stacking: B:H.61, B:H.61, B:F.377, B:H.378, B:H.378, B:F.425 Metal complexes: B:H.61, B:H.378 HEA.3: 34 residues within 4Å: Chain B: 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 C: I.34, P.69, I.72, L.73 Ligands: OXY.5 38 PLIP interactions: 34 interactions with chain B, 4 interactions with chain C, Hydrophobic interactions: B:W.236, B:V.243, B:V.243, B:I.247, B:T.309, B:A.313, B:V.320, B:V.320, B:F.348, B:I.356, B:L.358, B:L.358, B:V.373, B:V.373, B:F.377, B:F.377, B:V.380, B:L.381, B:L.381, B:L.381, C:I.34, C:P.69, C:I.72, C:L.73 Hydrogen bonds: B:Y.244, B:D.364 Water bridges: B:W.236, B:T.316, B:D.369, B:D.369, B:R.438, B:R.438 Salt bridges: B:H.368, B:R.438, B:R.439 pi-Stacking: B:H.290 pi-Cation interactions: B:H.240 Metal complexes: B:H.376

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

CU.4: 4 residues within 4Å: Chain B: H.240, H.290, H.291 Ligands: OXY.5 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.240, B:H.290, B:H.291

1 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.5: 6 residues within 4Å: Chain B: H.240, V.243, H.290, H.291 Ligands: HEA.3, CU.4 No protein-ligand interaction detected (PLIP)

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 4 residues within 4Å: Chain B: H.368, D.369 Chain C: S.197, E.198 6 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: B:H.368, B:D.369, C:E.198, H2O.5, H2O.9, H2O.10

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

CUA.8: 6 residues within 4Å: Chain C: H.161, C.196, E.198, C.200, H.204, M.207 7 PLIP interactions: 7 interactions with chain C Metal complexes: C:H.161, C:C.196, C:C.196, C:E.198, C:C.200, C:C.200, C: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.9: 16 residues within 4Å: Chain B: H.151, V.155, T.207, L.215 Chain D: W.34, Y.181, Y.182, A.184, F.186, T.187, I.188, F.198, G.202, F.203 Ligands: PGV.10, PGV.11 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: D:W.34, D:I.188, D:F.203, B:V.155, B:L.215, B:L.215 Hydrogen bonds: D:Y.181, D: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.10: 29 residues within 4Å: Chain B: F.94, P.95, R.96, M.97, M.100, H.151, L.152, V.155 Chain D: H.9, V.11, G.20, A.24, T.28, N.50, M.54, W.57, W.58, V.61, E.64, H.71, L.79, G.82, M.83, F.86, S.89, E.90, F.93 Ligands: PEK.9, PGV.11 15 PLIP interactions: 8 interactions with chain D, 7 interactions with chain B Hydrophobic interactions: D:A.24, D:T.28, D:W.57, D:W.57, D:W.57, D:W.58, D:F.86, D:F.93, B:H.151, B:L.152, B:V.155 Hydrogen bonds: B:R.96, B:R.96, B:M.97 Salt bridges: B:R.96 PGV.11: 23 residues within 4Å: Chain D: M.54, 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 Ligands: PEK.9, PGV.10 22 PLIP interactions: 22 interactions with chain D Hydrophobic interactions: D:W.58, D:W.58, D:W.58, D:W.58, D:I.62, D:F.86, D:F.86, D:I.210, D:I.210, D:T.213, D:F.214, D:F.214, D:F.214, D:F.214, D:F.233 Hydrogen bonds: D:S.65, D:R.221, D:F.233, D:G.234 Salt bridges: D:R.221, D:R.221, D:H.231

1 x ZN: ZINC ION(Non-covalent)

ZN.13: 4 residues within 4Å: Chain G: C.91, C.93, C.113, C.116 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.91, G:C.93, G:C.113, G:C.116

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

DMU.14: 11 residues within 4Å: Chain B: F.459, L.462 Chain E: L.117, W.120, Y.124 Chain M: L.51, L.52, G.55, W.56, Y.59, H.60 9 PLIP interactions: 5 interactions with chain E, 2 interactions with chain B, 2 interactions with chain M Hydrophobic interactions: E:L.117, E:W.120, E:W.120, E:W.120, B:F.459, B:L.462, M:L.51 Hydrogen bonds: E:Y.124, M:W.56

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 POLYPEPTIDE 6A2: A
CYTOCHROME C OXIDASE SUBUNIT 1: B
CYTOCHROME C OXIDASE SUBUNIT 2: C
CYTOCHROME C OXIDASE SUBUNIT 3: D
CYTOCHROME C OXIDASE SUBUNIT 4 ISOFORM 1: E
CYTOCHROME C OXIDASE SUBUNIT 5A: F
CYTOCHROME C OXIDASE SUBUNIT 5B: G
CYTOCHROME C OXIDASE SUBUNIT VIB ISOFORM 1: H
CYTOCHROME C OXIDASE POLYPEPTIDE VIC: I
CYTOCHROME C OXIDASE POLYPEPTIDE 7A1: J
CYTOCHROME C OXIDASE POLYPEPTIDE 7B: K
CYTOCHROME C OXIDASE SUBUNIT 7C: L
CYTOCHROME C OXIDASE POLYPEPTIDE 8H: M

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
N

C
O

D
P

E
Q

F
R

G
S

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 POLYPEPTIDE 6A2

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

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