SMTL ID : 5djq.2 (3 other biounits)

The structure of CBB3 cytochrome oxidase.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

HEM.1: 29 residues within 4Å: Chain A: E.122, Y.123, W.203, V.210, L.214, Y.251, H.257, H.258, S.276, L.279, S.283, S.320, T.321, G.324, P.325, M.327, A.328, N.333, S.336, H.337, T.342, H.345, V.346, G.349 Chain B: S.102 Ligands: HEM.2, CU.3, PEO.6, CA.7 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:Y.123, A:W.203, A:V.210, A:V.210, A:L.214, A:L.279, A:T.321, A:M.327, A:A.328, A:T.342, A:V.346 Hydrogen bonds: A:Y.123, A:N.333 Salt bridges: A:H.258, A:H.337 pi-Stacking: A:H.207 pi-Cation interactions: A:H.258 Metal complexes: A:H.345 HEM.2: 26 residues within 4Å: Chain A: M.29, G.32, V.33, I.35, A.36, R.57, H.60, T.61, V.64, I.65, E.122, Y.123, D.340, T.342, I.343, V.346, H.347, A.350, L.351, Y.395, R.437, G.441, F.444 Chain B: K.103 Ligands: HEM.1, CA.7 25 PLIP interactions: 24 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:M.29, A:V.33, A:I.35, A:I.35, A:A.36, A:V.64, A:V.64, A:I.65, A:I.65, A:Y.123, A:I.343, A:V.346, A:V.346, A:A.350, A:L.351, A:F.444 Hydrogen bonds: A:R.437 Salt bridges: A:R.57, A:R.57, B:K.103 pi-Stacking: A:H.60, A:H.347, A:Y.395 Metal complexes: A:H.60, A:H.347

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

CU.3: 5 residues within 4Å: Chain A: H.207, H.257, H.258 Ligands: HEM.1, PEO.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.207, A:H.257, A:H.258

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 6 residues within 4Å: Chain A: S.119, A.124, L.126, D.131, N.179, E.181 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:A.124, A:L.126, A:D.131 CA.7: 5 residues within 4Å: Chain A: R.57, E.122 Chain B: S.102 Ligands: HEM.1, HEM.2 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.102

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 5 residues within 4Å: Chain A: M.273, I.329, K.330, T.331 Chain C: Y.72 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:Y.72, A:K.330, A:T.331

1 x PEO: HYDROGEN PEROXIDE(Non-functional Binders)

PEO.6: 7 residues within 4Å: Chain A: H.207, V.210, H.257, H.258, H.345 Ligands: HEM.1, CU.3 No protein-ligand interaction detected (PLIP)

3 x HEC: HEME C(Covalent)

HEC.8: 26 residues within 4Å: Chain A: F.53, V.424, L.427 Chain B: E.63, C.65, C.68, H.69, T.105, G.106, P.107, L.109, Y.116, W.120, H.121, H.124, L.125, P.128, V.132, S.135, K.136, M.137, P.138, Y.140, M.188, L.192 Chain C: I.145 18 PLIP interactions: 15 interactions with chain B, 3 interactions with chain A, Hydrophobic interactions: B:E.63, B:P.107, B:L.109, B:W.120, B:L.125, B:V.132, B:M.137, B:P.138, B:Y.140, B:L.192, A:F.53, A:V.424, A:L.427 Hydrogen bonds: B:S.135 Salt bridges: B:H.124 pi-Stacking: B:H.69 pi-Cation interactions: B:H.124 Metal complexes: B:H.69 HEC.9: 27 residues within 4Å: Chain C: R.166, A.184, A.185, M.186, P.187, W.189, V.201, V.205, T.232, C.233, C.236, H.237, L.247, G.248, A.249, P.250, L.252, W.258, I.259, Y.260, G.261, L.267, T.270, I.271, R.275, G.277 Ligands: HEC.10 21 PLIP interactions: 21 interactions with chain C, Hydrophobic interactions: C:A.184, C:W.189, C:W.189, C:V.201, C:V.205, C:T.232, C:L.252, C:W.258, C:Y.260, C:L.267, C:T.270, C:I.271 Hydrogen bonds: C:I.259, C:Y.260, C:Y.260, C:G.261, C:G.277 Salt bridges: C:R.166, C:R.166 pi-Cation interactions: C:H.237 Metal complexes: C:H.237 HEC.10: 27 residues within 4Å: Chain B: R.115, Y.116, S.117 Chain C: Y.142, C.143, C.146, H.147, G.156, F.157, P.158, L.160, W.165, R.166, W.167, G.168, I.174, S.177, I.178, A.184, G.277, Q.278, M.279, P.280, Q.282, L.286, V.298 Ligands: HEC.9 21 PLIP interactions: 20 interactions with chain C, 1 interactions with chain B, Hydrophobic interactions: C:P.158, C:L.160, C:L.160, C:W.165, C:I.174, C:I.178, C:I.178, C:M.279, C:P.280, C:Q.282, C:L.286, C:V.298, B:Y.116 Hydrogen bonds: C:R.166, C:W.167, C:W.167, C:G.168, C:Y.260 Salt bridges: C:R.166 pi-Cation interactions: C:H.147 Metal complexes: C:H.147

1 x FC6: HEXACYANOFERRATE(3-)(Non-covalent)

FC6.11: 5 residues within 4Å: Chain C: Y.260, G.265, Q.266, Q.269, R.275 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.266, C:R.275

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Buschmann, S. et al., The structure of cbb3 cytochrome oxidase provides insights into proton pumping. Science (2010)

Release Date

2016-01-13

Peptides

Cbb3-type cytochrome c oxidase subunit CcoN1: A
Cbb3-type cytochrome c oxidase subunit II: B
Cbb3-type cytochrome c oxidase subunit CcoP1: C
Putative uncharacterized protein: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

D
O

Membrane

We predict this structure to be a membrane protein.
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Cbb3-type cytochrome c oxidase subunit CcoN1

Cbb3-type cytochrome c oxidase subunit II

Cbb3-type cytochrome c oxidase subunit CcoP1

Putative uncharacterized protein

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