SMTL ID : 3bvd.1

Structure of Surface-engineered Cytochrome ba3 Oxidase from Thermus thermophilus under Xenon Pressure, 100psi 5min

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.37 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

CU.1: 3 residues within 4Å: Chain A: H.239, H.288, H.289 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: 27 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, Y.139, P.388, F.391, H.392, V.395, A.396, T.400, W.434, M.438, M.441, R.455, R.456, A.457, L.483 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:L.38, A:A.49, A:Y.52, A:N.82, A:A.83, A:Y.139, A:P.388, A:F.391, A:F.391, A:V.395, A:A.396, A:W.434, A:L.483 Hydrogen bonds: A:R.456, A:A.457 Salt bridges: A:R.455, A:R.456 pi-Stacking: A:H.392 Metal complexes: A:H.78, A:H.392

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

HAS.3: 34 residues within 4Å: Chain A: Y.139, W.235, V.242, Y.243, W.245, L.246, Y.250, H.288, T.308, S.315, L.316, A.319, V.322, A.323, L.326, W.341, L.359, L.360, F.362, G.366, G.369, N.372, A.373, D.378, H.382, V.387, H.390, F.391, Q.394, V.395, V.399, R.455 Chain C: V.11, L.15 38 PLIP interactions: 35 interactions with chain A, 3 interactions with chain C, Hydrophobic interactions: A:W.235, 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:L.359, A:L.360, A:F.362, A:F.362, A:F.362, A:N.372, A:V.387, A:V.387, A:F.391, A:F.391, A:Q.394, A:V.395, A:V.399, C:V.11, C:V.11, C:L.15 Hydrogen bonds: A:Y.243, A:Y.243, A:N.383, A:R.455 Salt bridges: A:H.382, A:R.455, A:R.456 pi-Stacking: A:H.239 Metal complexes: A:H.390

7 x XE: XENON(Non-covalent)

XE.4: 3 residues within 4Å: Chain A: Y.139, W.235, G.238 No protein-ligand interaction detected (PLIP) XE.5: 3 residues within 4Å: Chain A: V.80, V.85, A.126 No protein-ligand interaction detected (PLIP) XE.6: 4 residues within 4Å: Chain A: F.141, Y.152, S.156, L.214 No protein-ligand interaction detected (PLIP) XE.7: 3 residues within 4Å: Chain A: S.156, V.159, V.207 No protein-ligand interaction detected (PLIP) XE.8: 4 residues within 4Å: Chain A: I.84, L.206, F.234 Ligands: XE.9 No protein-ligand interaction detected (PLIP) XE.9: 4 residues within 4Å: Chain A: F.234, T.237, G.238 Ligands: XE.8 No protein-ligand interaction detected (PLIP) XE.10: 3 residues within 4Å: Chain A: F.141, F.151, A.155 No protein-ligand interaction detected (PLIP)

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

CUA.11: 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

Luna, V.M. et al., Crystallographic Studies of Xe and Kr Binding within the Large Internal Cavity of Cytochrome ba3 from Thermus thermophilus: Structural Analysis and Role of Oxygen Transport Channels in the Heme-Cu Oxidases. Biochemistry (2008)

Release Date

2008-05-20

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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