SMTL ID : 4g71.1

Structure of Recombinant Cytochrome ba3 Oxidase mutant V236N from Thermus thermophilus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x CUB: CU(I)-S-MO(IV)(=O)O-NBIC CLUSTER(Covalent)

CUB.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: 25 residues within 4Å: Chain A: L.39, S.43, G.46, 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 23 PLIP interactions: 23 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 Hydrogen bonds: A:Y.72, A:R.457, A:A.458 Water bridges: A:Y.140, A:R.456, A:R.456 Salt bridges: A:R.456, A:R.457 pi-Cation interactions: A:H.393 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, H.240, N.243, Y.244, L.247, Y.251, H.289, H.290, T.309, S.316, L.317, A.320, A.324, L.327, W.342, V.357, L.360, F.363, 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: CUB.1, PER.4 31 PLIP interactions: 29 interactions with chain A, 2 interactions with chain C, Hydrophobic interactions: A:W.236, A:N.243, A:L.247, A:T.309, A:L.317, A:A.320, A:A.324, A:L.327, A:W.342, A:L.360, A:F.363, A:F.363, A:F.363, A:F.363, A:N.373, A:A.374, A:V.388, A:F.392, A:F.392, A:Q.395, A:V.396, C:V.11, C:L.15 Hydrogen bonds: A:Y.244, A:Y.244 Water bridges: A:H.290, 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, N.243, H.290 Ligands: CUB.1, HAS.3 No protein-ligand interaction detected (PLIP)

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

OLC.5: 5 residues within 4Å: Chain A: L.479, I.482, V.483, V.486 Ligands: OLC.13 Ligand excluded by PLIP OLC.6: 7 residues within 4Å: Chain A: W.348, L.429, W.433, L.437 Ligands: OLC.12, OLC.13, OLC.15 Ligand excluded by PLIP OLC.7: 7 residues within 4Å: Chain A: P.299, T.300, M.303, I.304, V.307, F.311 Chain B: A.42 Ligand excluded by PLIP OLC.8: 6 residues within 4Å: Chain A: K.147, W.150, W.218, 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: 4 residues within 4Å: Chain A: Y.168, L.171, D.172, R.175 Ligand excluded by PLIP OLC.11: 7 residues within 4Å: Chain A: L.171, W.174, R.175, K.178, L.198, G.535, F.538 Ligand excluded by PLIP OLC.12: 6 residues within 4Å: Chain A: A.471, V.475, F.476, L.479 Ligands: OLC.6, OLC.13 Ligand excluded by PLIP OLC.13: 5 residues within 4Å: Chain A: V.478, L.479 Ligands: OLC.5, OLC.6, OLC.12 Ligand excluded by PLIP OLC.14: 3 residues within 4Å: Chain A: L.216, L.222, V.223 Ligand excluded by PLIP OLC.15: 7 residues within 4Å: Chain A: R.344, W.348, L.361, W.433, F.436, L.437 Ligands: OLC.6 Ligand excluded by PLIP OLC.17: 4 residues within 4Å: Chain B: V.28, L.32, Y.35 Chain C: F.31 Ligand excluded by PLIP OLC.18: 12 residues within 4Å: Chain A: V.444, W.448, L.451 Chain B: G.120, R.141, P.142, E.144, Y.145 Chain C: V.29, R.33 Ligands: OLC.20, OLC.21 Ligand excluded by PLIP OLC.19: 7 residues within 4Å: Chain B: A.13, Y.14, G.17, W.18, F.21 Chain C: L.9, I.12 Ligand excluded by PLIP OLC.20: 9 residues within 4Å: Chain A: A.443, H.447 Chain C: F.22, G.25, A.28, V.29, A.32 Ligands: OLC.18, OLC.21 Ligand excluded by PLIP OLC.21: 6 residues within 4Å: Chain A: L.361, P.365 Chain C: T.18, V.21 Ligands: OLC.18, OLC.20 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

Li, Y. et al., Structure of Recombinant Cytochrome ba3 Oxidase mutant V236N 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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