SMTL ID : 3s8f.1

1.8 A structure of ba3 cytochrome c oxidase from Thermus thermophilus in lipid environment

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

CU.1: 4 residues within 4Å: Chain A: H.240, H.289, H.290 Ligands: PER.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.240, A:H.289, A:H.290

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.2: 25 residues within 4Å: Chain A: L.39, G.46, P.47, Q.49, A.50, Y.53, Y.72, L.76, H.79, N.83, A.84, L.139, Y.140, F.392, H.393, V.396, A.397, T.401, W.435, M.439, M.442, R.456, R.457, A.458, L.484 26 PLIP interactions: 26 interactions with chain A, Hydrophobic interactions: A:L.39, A:Q.49, A:Y.53, A:N.83, A:A.84, A:Y.140, A:Y.140, A:F.392, A:F.392, A:V.396, A:A.397, A:W.435, A:W.435, A:L.484, A:L.484 Hydrogen bonds: A:Y.72, A:R.457, A:A.458 Water bridges: A:Y.53, A:Y.140, A:R.456, A:R.456 Salt bridges: A:R.456, A:R.457 Metal complexes: A:H.79, A:H.393

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

HAS.3: 36 residues within 4Å: Chain A: Y.140, W.236, V.243, Y.244, W.246, L.247, Y.251, H.289, H.290, T.309, S.316, L.317, A.320, V.323, A.324, L.327, V.357, L.360, L.361, F.363, I.364, G.367, G.370, I.371, N.373, A.374, D.379, H.383, V.388, H.391, F.392, Q.395, V.396, R.456 Chain C: V.11 Ligands: PER.4 39 PLIP interactions: 37 interactions with chain A, 2 interactions with chain C, Hydrophobic interactions: A:W.236, A:V.243, A:V.243, A:V.243, A:W.246, A:W.246, A:L.247, A:T.309, A:L.317, A:A.320, A:V.323, A:A.324, A:L.327, A:V.357, A:L.360, A:L.361, A:F.363, A:F.363, A:F.363, A:I.364, A:I.371, A:N.373, A:A.374, A:F.392, A:F.392, A:Q.395, A:V.396, C:V.11, C:V.11 Hydrogen bonds: A:Y.244, A:Y.244 Water bridges: A:H.290, A:N.384, A:N.384, A:R.456 Salt bridges: A:H.383, A:R.456, A:R.457 Metal complexes: A:H.391

1 x PER: PEROXIDE ION(Non-covalent)

PER.4: 5 residues within 4Å: Chain A: H.240, V.243, H.290 Ligands: CU.1, HAS.3 No protein-ligand interaction detected (PLIP)

16 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLC.5: 14 residues within 4Å: Chain A: P.365, M.440, A.443, V.444, H.447, L.451 Chain C: V.21, F.22, G.25, V.26, V.29, A.32 Ligands: OLC.18, OLC.21 Ligand excluded by PLIP OLC.6: 4 residues within 4Å: Chain A: L.434, I.482, V.486 Ligands: OLC.13 Ligand excluded by PLIP OLC.7: 8 residues within 4Å: Chain A: W.348, V.354, L.429, W.433, L.434, L.437 Ligands: OLC.12, OLC.13 Ligand excluded by PLIP OLC.8: 5 residues within 4Å: Chain A: K.147, W.150, S.219, F.220, G.221 Ligand excluded by PLIP OLC.9: 1 residues within 4Å: Chain A: W.118 Ligand excluded by PLIP OLC.10: 5 residues within 4Å: Chain A: Y.168, L.171, D.172, R.175 Ligands: OLC.11 Ligand excluded by PLIP OLC.11: 5 residues within 4Å: Chain A: W.174, R.175, K.178, G.535 Ligands: OLC.10 Ligand excluded by PLIP OLC.12: 8 residues within 4Å: Chain A: A.471, V.472, V.475, F.476, L.479 Ligands: OLC.7, OLC.13, OLC.15 Ligand excluded by PLIP OLC.13: 6 residues within 4Å: Chain A: V.56, V.478, L.479 Ligands: OLC.6, OLC.7, OLC.12 Ligand excluded by PLIP OLC.14: 1 residues within 4Å: Chain A: L.222 Ligand excluded by PLIP OLC.15: 10 residues within 4Å: Chain A: R.344, L.346, W.348, L.358, L.361, W.433, L.437, M.440, V.444 Ligands: OLC.12 Ligand excluded by PLIP OLC.17: 6 residues within 4Å: Chain B: V.28, L.32, Y.35, T.39 Chain C: Y.27, F.31 Ligand excluded by PLIP OLC.18: 12 residues within 4Å: Chain A: V.444, W.448, L.451, L.452 Chain B: G.120, R.141, P.142, E.144, Y.145 Chain C: R.33 Ligands: OLC.5, OLC.21 Ligand excluded by PLIP OLC.19: 10 residues within 4Å: Chain B: A.13, Y.14, G.17, W.18, F.21 Chain C: L.9, I.12, L.13, T.16, L.20 Ligand excluded by PLIP OLC.20: 6 residues within 4Å: Chain A: P.299, T.300, I.304, V.307 Chain B: L.37, A.42 Ligand excluded by PLIP OLC.21: 7 residues within 4Å: Chain A: P.365 Chain C: V.14, T.18, V.21, F.22 Ligands: OLC.5, OLC.18 Ligand excluded by PLIP

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

CUA.16: 6 residues within 4Å: Chain B: H.114, C.149, Q.151, C.153, H.157, M.160 7 PLIP interactions: 7 interactions with chain B Metal complexes: B:H.114, B:C.149, B:C.149, B:Q.151, B:C.153, B:C.153, B:H.157

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tiefenbrunn, T. et al., High resolution structure of the ba3 cytochrome c oxidase from Thermus thermophilus in a lipidic environment. Plos One (2011)

Release Date

2011-08-03

Peptides

Cytochrome c oxidase subunit 1: A
Cytochrome c oxidase subunit 2: B
Cytochrome c oxidase polypeptide 2A: 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 subunit 1

Cytochrome c oxidase subunit 2

Cytochrome c oxidase polypeptide 2A

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