SMTL ID : 1occ.1

STRUCTURE OF BOVINE HEART CYTOCHROME C OXIDASE AT THE FULLY OXIDIZED STATE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-2-2-2-2-2-2-2-2-2-2-2-2-2-mer

Ligands

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

CU.1: 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 CU.5: 6 residues within 4Å: Chain B: H.161, C.196, E.198, C.200, M.207 Ligands: CU.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.161, B:C.196, B:C.200 CU.6: 5 residues within 4Å: Chain B: C.196, E.198, C.200, H.204 Ligands: CU.5 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.196, B:E.198, B:C.200, B:H.204 CU.8: 3 residues within 4Å: Chain N: H.240, H.290, H.291 3 PLIP interactions: 3 interactions with chain N Metal complexes: N:H.240, N:H.290, N:H.291 CU.12: 6 residues within 4Å: Chain O: H.161, C.196, E.198, C.200, M.207 Ligands: CU.13 3 PLIP interactions: 3 interactions with chain O Metal complexes: O:H.161, O:C.196, O:C.200 CU.13: 5 residues within 4Å: Chain O: C.196, E.198, C.200, H.204 Ligands: CU.12 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.196, O:E.198, O:C.200, O:H.204

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: H.368, D.369 Chain B: E.198 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Metal complexes: A:H.368, A:D.369, B:E.198 MG.9: 3 residues within 4Å: Chain N: H.368, D.369 Chain O: E.198 3 PLIP interactions: 2 interactions with chain N, 1 interactions with chain O Metal complexes: N:H.368, N:D.369, O:E.198

4 x HEA: HEME-A(Covalent)(Non-covalent)

HEA.3: 34 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, T.424, F.425, Q.428, R.438, R.439, Y.440, M.468 32 PLIP interactions: 32 interactions with chain A, Hydrophobic interactions: A:A.24, A:I.37, A:V.58, A:V.58, A:A.62, A:M.65, A:I.66, A:V.70, A:I.73, A:V.374, A:F.377, A:L.381, A:V.386, A:V.386, A:F.393, A:F.393, A:T.424, A:F.425 Hydrogen bonds: A:R.38, A:Y.54, A:W.126, A:Y.371, A:S.382, A:Q.428, A:R.439, A:Y.440 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.4: 29 residues within 4Å: Chain A: W.126, W.236, V.243, Y.244, I.247, H.290, H.291, T.309, A.313, T.316, G.317, 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 22 PLIP interactions: 20 interactions with chain A, 2 interactions with chain B, Hydrophobic interactions: A:W.236, A:V.243, A:Y.244, A:I.247, A:T.309, A:A.313, A:F.348, A:I.356, A:V.373, A:F.377, A:F.377, A:V.380, A:L.381, B:I.34, B:P.69 Hydrogen bonds: A:W.126, A:Y.244 Salt bridges: A:H.291, A:H.368, A:R.438 pi-Cation interactions: A:H.240 Metal complexes: A:H.376 HEA.10: 34 residues within 4Å: Chain N: 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, T.424, F.425, Q.428, R.438, R.439, Y.440, M.468 32 PLIP interactions: 32 interactions with chain N, Hydrophobic interactions: N:A.24, N:I.37, N:V.58, N:V.58, N:A.62, N:M.65, N:I.66, N:V.70, N:I.73, N:V.374, N:F.377, N:L.381, N:V.386, N:V.386, N:F.393, N:F.393, N:T.424, N:F.425 Hydrogen bonds: N:R.38, N:Y.54, N:W.126, N:Y.371, N:S.382, N:Q.428, N:R.439, N:Y.440 Salt bridges: N:R.438, N:R.439 pi-Stacking: N:F.377, N:F.425 Metal complexes: N:H.61, N:H.378 HEA.11: 29 residues within 4Å: Chain N: W.126, W.236, V.243, Y.244, I.247, H.290, H.291, T.309, A.313, T.316, G.317, 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 O: I.34, P.69 22 PLIP interactions: 2 interactions with chain O, 20 interactions with chain N, Hydrophobic interactions: O:I.34, O:P.69, N:W.236, N:V.243, N:Y.244, N:I.247, N:T.309, N:A.313, N:F.348, N:I.356, N:V.373, N:F.377, N:F.377, N:V.380, N:L.381 Hydrogen bonds: N:W.126, N:Y.244 Salt bridges: N:H.291, N:H.368, N:R.438 pi-Cation interactions: N:H.240 Metal complexes: N:H.376

2 x ZN: ZINC ION(Non-covalent)

ZN.7: 5 residues within 4Å: Chain F: C.60, C.62, C.82, S.84, C.85 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.60, F:C.62, F:C.82, F:C.85 ZN.14: 5 residues within 4Å: Chain S: C.60, C.62, C.82, S.84, C.85 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:C.60, S:C.62, S:C.82, S:C.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tsukihara, T. et al., The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 A. Science (1996)

Release Date

1996-12-07

Peptides

CYTOCHROME C OXIDASE: AN
CYTOCHROME C OXIDASE: BO
CYTOCHROME C OXIDASE: CP
CYTOCHROME C OXIDASE: DQ
CYTOCHROME C OXIDASE: ER
CYTOCHROME C OXIDASE: FS
CYTOCHROME C OXIDASE: GT
CYTOCHROME C OXIDASE: HU
CYTOCHROME C OXIDASE: IV
CYTOCHROME C OXIDASE: JW
CYTOCHROME C OXIDASE: KX
CYTOCHROME C OXIDASE: LY
CYTOCHROME C OXIDASE: MZ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

N
N

B
B

O
O

C
C

P
P

D
D

Q
Q

E
E

R
R

F
F

S
S

G
G

T
T

H
H

U
U

I
I

V
V

J
J

W
W

K
K

X
X

L
L

Y
Y

M
M

Z
Z

Membrane

We predict this structure to be a membrane protein.
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CYTOCHROME C OXIDASE

CYTOCHROME C OXIDASE

CYTOCHROME C OXIDASE

CYTOCHROME C OXIDASE

CYTOCHROME C OXIDASE

CYTOCHROME C OXIDASE

CYTOCHROME C OXIDASE

CYTOCHROME C OXIDASE

CYTOCHROME C OXIDASE

CYTOCHROME C OXIDASE

CYTOCHROME C OXIDASE

CYTOCHROME C OXIDASE

CYTOCHROME C OXIDASE

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