SMTL ID : 4gp4.1

Structure of Recombinant Cytochrome ba3 Oxidase mutant Y133F from Thermus thermophilus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 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.239, H.288, H.289 Ligands: PER.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.239, A:H.288, A:H.289

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

HEM.2: 26 residues within 4Å: Chain A: L.38, S.42, G.45, P.46, Q.48, A.49, Y.52, Y.71, L.75, H.78, N.82, A.83, L.138, F.139, F.391, H.392, V.395, A.396, T.400, W.434, M.438, M.441, R.455, R.456, A.457, L.483 25 PLIP interactions: 25 interactions with chain A, Hydrophobic interactions: A:L.38, A:Q.48, A:Y.52, A:N.82, A:A.83, A:F.139, A:F.139, A:F.391, A:V.395, A:A.396, A:W.434, A:L.483, A:L.483 Hydrogen bonds: A:Y.71, A:R.456, A:A.457 Water bridges: A:F.139, A:R.455, A:R.455 Salt bridges: A:R.455, A:R.456 pi-Stacking: A:F.391 pi-Cation interactions: A:H.392 Metal complexes: A:H.78, A:H.392

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

HAS.3: 35 residues within 4Å: Chain A: F.139, W.235, V.242, Y.243, W.245, L.246, Y.250, H.288, H.289, T.308, S.315, L.316, A.319, V.322, A.323, L.326, W.341, V.356, L.359, F.362, G.366, G.369, I.370, N.372, A.373, D.378, H.382, H.390, F.391, Q.394, V.395, R.455 Chain C: V.11, L.15 Ligands: PER.4 38 PLIP interactions: 2 interactions with chain C, 36 interactions with chain A, Hydrophobic interactions: C:V.11, C:L.15, A:W.235, A:V.242, A:V.242, A:V.242, A:W.245, A:W.245, A:L.246, A:T.308, A:L.316, A:A.319, A:V.322, A:A.323, A:L.326, A:W.341, A:V.356, A:L.359, A:F.362, A:F.362, A:F.362, A:F.362, A:I.370, A:N.372, A:F.391, A:F.391, A:Q.394, A:V.395 Hydrogen bonds: A:Y.243, A:Y.243 Water bridges: A:H.289, A:N.383, A:R.455, A:R.455 Salt bridges: A:H.382, A:R.455, A:R.456 Metal complexes: A:H.390

1 x PER: PEROXIDE ION(Non-covalent)

PER.4: 6 residues within 4Å: Chain A: H.239, V.242, H.288, H.289 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: 13 residues within 4Å: Chain A: P.364, M.439, V.443, H.446, L.450 Chain C: V.21, F.22, G.25, A.28, V.29, A.32 Ligands: OLC.6, OLC.20 Ligand excluded by PLIP OLC.6: 7 residues within 4Å: Chain A: L.360, I.363 Chain C: V.14, T.18, V.21 Ligands: OLC.5, OLC.20 Ligand excluded by PLIP OLC.7: 5 residues within 4Å: Chain A: L.433, I.481, V.482, V.485 Ligands: OLC.15 Ligand excluded by PLIP OLC.8: 7 residues within 4Å: Chain A: W.347, L.428, A.429, W.432, L.436 Ligands: OLC.14, OLC.15 Ligand excluded by PLIP OLC.9: 7 residues within 4Å: Chain A: P.298, T.299, M.302, I.303, V.306 Chain B: L.37, A.42 Ligand excluded by PLIP OLC.10: 3 residues within 4Å: Chain A: W.149, S.218, F.219 Ligand excluded by PLIP OLC.11: 1 residues within 4Å: Chain A: W.117 Ligand excluded by PLIP OLC.12: 5 residues within 4Å: Chain A: Y.167, L.170, D.171, R.174 Ligands: OLC.13 Ligand excluded by PLIP OLC.13: 7 residues within 4Å: Chain A: L.170, W.173, R.174, K.177, G.534, F.537 Ligands: OLC.12 Ligand excluded by PLIP OLC.14: 7 residues within 4Å: Chain A: A.470, V.474, F.475, L.478 Ligands: OLC.8, OLC.15, OLC.17 Ligand excluded by PLIP OLC.15: 7 residues within 4Å: Chain A: V.55, V.474, V.477, L.478 Ligands: OLC.7, OLC.8, OLC.14 Ligand excluded by PLIP OLC.16: 2 residues within 4Å: Chain A: V.211, V.222 Ligand excluded by PLIP OLC.17: 7 residues within 4Å: Chain A: R.343, W.347, W.432, F.435, L.436, I.440 Ligands: OLC.14 Ligand excluded by PLIP OLC.19: 5 residues within 4Å: Chain B: V.28, L.32, Y.35 Chain C: Y.27, F.31 Ligand excluded by PLIP OLC.20: 10 residues within 4Å: Chain A: W.447, L.450 Chain B: R.141, P.142, E.144, Y.145 Chain C: V.29, R.33 Ligands: OLC.5, OLC.6 Ligand excluded by PLIP OLC.21: 8 residues within 4Å: Chain B: A.13, Y.14, G.17, F.21 Chain C: L.9, I.12, L.13, L.20 Ligand excluded by PLIP

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

CUA.18: 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

McDonald, W. et al., Ligand Access to the Active Site in Thermus thermophilusba(3) and Bovine Heart aa(3) Cytochrome Oxidases. Biochemistry (2013)

Release Date

2013-01-16

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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