SMTL ID : 4g7r.1

Structure of Recombinant Cytochrome ba3 Oxidase mutant V236A from Thermus thermophilus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.05 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

CU.1: 5 residues within 4Å: Chain A: H.240, H.289, H.290 Ligands: HAS.3, 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: 27 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, P.389, F.392, H.393, V.396, A.397, T.401, W.435, M.439, M.442, R.456, R.457, A.458, L.484 24 PLIP interactions: 24 interactions with chain A, Hydrophobic interactions: A:L.39, A:Q.49, A:A.50, 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:V.396, A:A.397, A:W.435, A:W.435, A:L.484 Hydrogen bonds: A:Y.72, A:Y.140, A:R.457, A:A.458 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: 38 residues within 4Å: Chain A: Y.140, W.236, A.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, W.342, 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, L.15 Ligands: CU.1, PER.4 33 PLIP interactions: 32 interactions with chain A, 1 interactions with chain C, Hydrophobic interactions: A:W.236, A:A.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:W.342, A:L.360, A:L.361, A:F.363, A:F.363, A:F.363, A:I.364, A:I.364, A:I.371, A:N.373, A:F.392, A:F.392, A:Q.395, A:V.396, C:L.15 Hydrogen bonds: A:Y.244, A:Y.244 Water bridges: A:H.290 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, A.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: 14 residues within 4Å: Chain A: P.365, M.440, V.444, H.447, L.451 Chain C: V.21, F.22, G.25, V.26, A.28, V.29, A.32 Ligands: OLC.17, OLC.19 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:P.365, A:P.365, A:V.444, A:H.447, A:L.451, C:F.22, C:F.22 OLC.6: 4 residues within 4Å: Chain A: L.479, I.482, V.483 Ligands: OLC.13 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.479, A:V.483 OLC.7: 9 residues within 4Å: Chain A: W.348, V.354, L.429, W.433, L.434, L.437 Ligands: OLC.12, OLC.13, OLC.15 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.433, A:W.433, A:L.434, A:L.437 OLC.8: 7 residues within 4Å: Chain A: P.299, T.300, M.303, I.304, V.307 Chain B: L.37, A.42 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.299, A:T.300, A:I.304, A:V.307, B:L.37 OLC.9: 6 residues within 4Å: Chain A: K.147, W.150, L.154, S.219, F.220, G.221 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.150, A:W.150, A:L.154, A:F.220, A:F.220 Hydrogen bonds: A:K.147, A:K.147 OLC.10: 1 residues within 4Å: Chain A: W.118 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.118, A:W.118 OLC.11: 4 residues within 4Å: Chain A: Y.168, L.171, D.172, R.175 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.172, A:R.175, A:R.175, A:R.175 OLC.12: 6 residues within 4Å: Chain A: A.471, V.472, V.475, L.479 Ligands: OLC.7, OLC.13 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.472, A:L.479 OLC.13: 4 residues within 4Å: Chain A: L.479 Ligands: OLC.6, OLC.7, OLC.12 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.479, A:L.479 OLC.14: 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.15: 6 residues within 4Å: Chain A: R.344, W.348, F.436, L.437, I.441 Ligands: OLC.7 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.348, A:W.348, A:W.348, A:F.436, A:L.437, A:I.441 Water bridges: A:R.344 OLC.17: 10 residues within 4Å: Chain A: W.448, L.451 Chain B: E.119, G.120, R.141, Y.145 Chain C: V.29, R.33 Ligands: OLC.5, OLC.19 6 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: A:W.448, A:L.451, C:V.29, C:R.33 Hydrogen bonds: B:R.141 Salt bridges: B:R.141 OLC.18: 6 residues within 4Å: Chain B: A.13, Y.14, G.17, W.18, F.21 Chain C: L.9 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:Y.14, B:F.21, C:L.9 OLC.19: 6 residues within 4Å: Chain A: I.364 Chain C: V.14, T.18, F.22 Ligands: OLC.5, OLC.17 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:V.14, C:T.18, C:F.22, A:I.364 Water bridges: A:W.448 OLC.20: 5 residues within 4Å: Chain B: V.28, L.32, Y.35 Chain C: Y.27, F.31 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:V.28, B:L.32, B:Y.35 Hydrogen bonds: C:Y.27

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

Li, Y. et al., Structure of Recombinant Cytochrome ba3 Oxidase mutant V236A 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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