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

Structure of caa3-type cytochrome oxidase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.36 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x 5PL: (1R,4S,6R)-6-({[2-(ACETYLAMINO)-2-DEOXY-ALPHA-D-GLUCOPYRANOSYL]OXY}METHYL)-4-HYDROXY-1-{[(15-METHYLHEXADECANOYL)OXY]METHYL}-4-OXIDO-7-OXO-3,5-DIOXA-8-AZA-4-PHOSPHAHEPTACOS-1-YL 15-METHYLHEXADECANOATE(Non-covalent)

5PL.1: 28 residues within 4Å: Chain A: L.106, R.108, V.109, F.165, L.169, F.568, F.589, A.590, L.593, W.596, A.597, D.600, E.601, A.617, M.621, F.624, E.628, L.735, L.738, I.742, F.745, Q.753, K.758, N.763, G.765, T.766, A.769, Y.773 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:L.106, A:L.106, A:L.169, A:F.568, A:F.568, A:F.589, A:A.590, A:W.596, A:W.596, A:F.624, A:F.624, A:L.735, A:L.738, A:I.742, A:I.742, A:A.769 Hydrogen bonds: A:W.596, A:E.601, A:E.601, A:Q.753, A:N.763 Water bridges: A:R.108, A:R.108 Salt bridges: A:R.108, A:R.108

2 x HAS: HEME-AS(Non-covalent)

HAS.2: 31 residues within 4Å: Chain A: F.37, F.39, A.40, G.43, V.44, S.46, I.49, R.50, Y.66, L.70, H.73, G.74, M.77, L.78, G.138, W.139, Y.380, F.386, H.387, L.390, M.391, T.433, F.434, Q.437, R.447, R.448, Y.449, A.470, L.473, G.474, G.477 27 PLIP interactions: 27 interactions with chain A, Hydrophobic interactions: A:F.37, A:F.39, A:F.39, A:A.40, A:V.44, A:I.49, A:L.70, A:M.77, A:L.78, A:F.386, A:L.390, A:T.433, A:A.470 Hydrogen bonds: A:R.50, A:W.139, A:Y.380, A:Q.437, A:R.448, A:Y.449 Water bridges: A:R.447, A:R.447 Salt bridges: A:R.447, A:R.448 pi-Stacking: A:F.386, A:F.434 Metal complexes: A:H.73, A:H.387 HAS.3: 40 residues within 4Å: Chain A: W.139, W.246, V.253, Y.254, L.257, H.299, H.300, T.318, I.321, A.322, T.325, G.326, L.329, F.330, F.357, L.358, G.361, I.362, G.364, V.365, M.366, L.367, S.368, D.373, H.377, V.382, H.385, F.386, V.389, L.390, S.394, R.447 Chain B: V.42, F.45, S.46, I.49, P.91, I.94, V.95, L.98 38 PLIP interactions: 31 interactions with chain A, 6 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: A:W.246, A:V.253, A:V.253, A:V.253, A:L.257, A:T.318, A:A.322, A:T.325, A:L.329, A:F.330, A:F.357, A:L.358, A:I.362, A:I.362, A:L.367, A:V.382, A:F.386, A:F.386, A:V.389, A:L.390, A:L.390, B:F.45, B:I.49, B:P.91, B:I.94, B:V.95, B:L.98 Hydrogen bonds: A:W.139, A:Y.254 Water bridges: A:T.325, A:D.378, A:D.378 Salt bridges: A:H.377, A:R.447 pi-Stacking: A:H.299 pi-Cation interactions: A:H.250 Metal complexes: A:H.385, H2O.3

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

CU.4: 3 residues within 4Å: Chain A: H.250, H.299, H.300 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.250, A:H.299, A:H.300, H2O.3, H2O.3

1 x 4AG: (2R)-3-HYDROXYPROPANE-1,2-DIYL DIHEXADECANOATE(Non-covalent)

4AG.5: 12 residues within 4Å: Chain A: M.366, L.435, Y.438, A.439, Y.442, L.443, A.457 Chain B: R.21, A.23, T.25, Y.43, S.46 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.435, A:L.435, A:Y.438, A:A.439, A:Y.442, A:Y.442, A:Y.442, A:L.443, A:A.457, B:Y.43 Salt bridges: B:R.21

2 x 7E8: (2R)-2,3-DIHYDROXYPROPYL (7Z)-TETRADEC-7-ENOATE(Non-covalent)

7E8.6: 11 residues within 4Å: Chain A: L.29, T.32, F.36, F.37, A.40, M.409, T.410, I.481, M.484, L.488, P.511 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.29, A:T.32, A:A.40, A:I.481, A:L.488 7E8.7: 7 residues within 4Å: Chain A: Q.65, Q.68, I.69, L.72, L.125, Y.128, F.129 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.72, A:Y.128, A:F.129 Hydrogen bonds: A:Q.68 Water bridges: A:Q.68

1 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 3 residues within 4Å: Chain A: H.377, D.378 Chain B: E.199 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.377, A:D.378, H2O.2, H2O.4, H2O.4

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

CUA.9: 6 residues within 4Å: Chain B: H.162, C.197, E.199, C.201, H.205, M.208 7 PLIP interactions: 7 interactions with chain B Metal complexes: B:H.162, B:C.197, B:C.197, B:E.199, B:C.201, B:C.201, B:H.205

1 x HEC: HEME C(Covalent)

HEC.10: 25 residues within 4Å: Chain B: Q.125, F.126, W.127, N.141, N.246, C.247, C.250, H.251, I.262, P.264, W.269, R.272, L.275, G.276, A.277, L.287, W.290, I.291, K.298, V.301, M.303, P.304, F.306, L.317, L.321 23 PLIP interactions: 23 interactions with chain B, Hydrophobic interactions: B:W.127, B:N.246, B:P.264, B:W.269, B:W.269, B:L.287, B:W.290, B:I.291, B:V.301, B:M.303, B:F.306, B:F.306, B:L.321 Hydrogen bonds: B:F.126, B:N.141, B:G.276, B:A.277 Salt bridges: B:R.272, B:K.298 pi-Stacking: B:H.251, B:H.251, B:H.251 Metal complexes: B:H.251

1 x 7E9: 1,3-DIHYDROXYPROPAN-2-YL (Z)-TETRADEC-7-ENOATE(Non-covalent)

7E9.11: 1 residues within 4Å: Chain B: Y.43 No protein-ligand interaction detected (PLIP)

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.12: 3 residues within 4Å: Chain A: T.308 Chain C: H.63, H.64 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lyons, J.A. et al., Structural Insights Into Electron Transfer in Caa3-Type Cytochrome Oxidases. Nature (2012)

Release Date

2012-05-23

Peptides

CYTOCHROME C OXIDASE POLYPEPTIDE I+III: A
CYTOCHROME C OXIDASE SUBUNIT 2: B
CAA3-TYPE CYTOCHROME OXIDASE SUBUNIT IV: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

We predict this structure to be a membrane protein.
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CYTOCHROME C OXIDASE POLYPEPTIDE I+III

CYTOCHROME C OXIDASE SUBUNIT 2

CAA3-TYPE CYTOCHROME OXIDASE SUBUNIT IV

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