SMTL ID : 4g7s.1

Structure of Recombinant Cytochrome ba3 Oxidase mutant V236I from Thermus thermophilus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 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: 26 residues within 4Å: Chain A: L.39, S.43, 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, I.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 35 PLIP interactions: 34 interactions with chain A, 1 interactions with chain C, Hydrophobic interactions: A:W.236, A:I.243, A:I.243, A:W.246, A:W.246, A:L.247, A:T.309, A:L.317, A:A.320, A:V.323, 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 Hydrogen bonds: A:Y.244, A:Y.244 Water bridges: 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, I.243, H.290 Ligands: CU.1, HAS.3 No protein-ligand interaction detected (PLIP)

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

OLC.5: 3 residues within 4Å: Chain A: I.482, V.486 Ligands: OLC.11 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.482, A:I.482, A:V.486 OLC.6: 8 residues within 4Å: Chain A: W.348, V.354, L.429, W.433, L.434, L.437 Ligands: OLC.10, OLC.11 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.433, A:W.433, A:L.434, A:L.437 OLC.7: 3 residues within 4Å: Chain A: W.150, S.219, F.220 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.220, A:F.220 OLC.8: 1 residues within 4Å: Chain A: W.118 No protein-ligand interaction detected (PLIP) OLC.9: 6 residues within 4Å: Chain A: Y.168, L.171, W.174, R.175, G.535, F.538 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.168, A:Y.168, A:L.171 Hydrogen bonds: A:R.175 Water bridges: A:G.535 Salt bridges: A:R.175 OLC.10: 7 residues within 4Å: Chain A: A.471, V.472, V.475, F.476 Ligands: OLC.6, OLC.11, OLC.13 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.472, A:V.472, A:V.475, A:F.476 OLC.11: 6 residues within 4Å: Chain A: V.475, V.478, L.479 Ligands: OLC.5, OLC.6, OLC.10 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.475, A:V.478, A:L.479, A:L.479 OLC.12: 3 residues within 4Å: Chain A: L.216, L.222, V.223 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.216, A:L.222, A:V.223 OLC.13: 7 residues within 4Å: Chain A: R.344, W.348, W.433, F.436, L.437, V.444 Ligands: OLC.10 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.348, A:W.348, A:W.433, A:W.433, A:F.436, A:L.437, A:V.444 Hydrogen bonds: A:L.346 OLC.15: 5 residues within 4Å: Chain B: V.28, L.32, Y.35 Chain C: Y.27, F.31 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:V.28, B:V.28, B:L.32, B:Y.35, B:Y.35 Hydrogen bonds: C:Y.27 OLC.16: 8 residues within 4Å: Chain A: W.448, L.451 Chain B: R.141, P.142, E.144, Y.145 Chain C: R.33 Ligands: OLC.19 6 PLIP interactions: 1 interactions with chain C, 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: C:R.33, A:L.451 Hydrogen bonds: B:R.141, B:P.142 Water bridges: B:R.146 Salt bridges: B:R.141 OLC.17: 7 residues within 4Å: Chain B: A.13, Y.14, G.17, W.18, F.21 Chain C: L.9, I.12 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:F.21, C:L.9 Hydrogen bonds: B:Y.14, B:G.17 OLC.18: 7 residues within 4Å: Chain A: P.299, T.300, M.303, I.304, V.307 Chain B: L.37, A.42 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.299, A:T.300, A:M.303, A:V.307, A:V.307, B:L.37 OLC.19: 10 residues within 4Å: Chain A: P.365, A.443, H.447, L.451 Chain C: V.21, F.22, G.25, V.29, A.32 Ligands: OLC.16 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:P.365, A:A.443, A:H.447, A:L.451, C:F.22, C:F.22 OLC.20: 4 residues within 4Å: Chain A: L.361 Chain C: V.14, T.18, V.21 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.14, C:T.18, C:V.21

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

CUA.14: 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

Li, Y. et al., Structure of Recombinant Cytochrome ba3 Oxidase mutant V236I from Thermus thermophilus. To be Published

Release Date

2013-07-24

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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