SMTL ID : 5ndc.1

Structure of ba3-type cytochrome c oxidase from Thermus thermophilus by serial femtosecond crystallography

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 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.240, H.289, H.290 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.240, A:H.289, A:H.290, H2O.2

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

HEM.2: 25 residues within 4Å: Chain A: L.39, 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 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:F.392, A:F.392, A:V.396, A:A.397, A:W.435, A:L.484, A:L.484 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 Metal complexes: A:H.79, A:H.393

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

HAS.3: 31 residues within 4Å: Chain A: Y.140, W.236, V.243, Y.244, W.246, L.247, Y.251, H.289, H.290, T.309, S.316, L.317, A.320, A.324, V.357, L.360, L.361, F.363, I.364, G.367, G.370, N.373, A.374, D.379, H.383, V.388, H.391, F.392, Q.395, V.396, R.456 33 PLIP interactions: 32 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:W.236, A:V.243, A:V.243, A:V.243, A:W.246, A:W.246, A:L.247, A:T.309, A:L.317, A:A.320, A:A.324, A:V.357, A:L.360, A:L.361, A:F.363, A:F.363, A:I.364, A:N.373, A:A.374, A:F.392, A:F.392, A:Q.395, A:V.396 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, H2O.2

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

OLC.4: 2 residues within 4Å: Chain A: W.348, W.433 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.433, A:W.433 OLC.5: 4 residues within 4Å: Chain A: K.147, W.150, S.219, F.220 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.150, A:F.220 Hydrogen bonds: A:K.147, A:K.147 OLC.6: 3 residues within 4Å: Chain A: K.26, W.114, W.118 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.26, A:K.26 OLC.7: 5 residues within 4Å: Chain A: W.164, W.174, R.175, F.201, F.538 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.201 Salt bridges: A:R.175 OLC.8: 2 residues within 4Å: Chain A: V.475 Ligands: OLC.9 No protein-ligand interaction detected (PLIP) OLC.9: 2 residues within 4Å: Chain A: L.479 Ligands: OLC.8 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.479 OLC.10: 1 residues within 4Å: Chain A: L.222 No protein-ligand interaction detected (PLIP) OLC.11: 3 residues within 4Å: Chain A: W.348, L.361, L.437 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.348, A:W.348, A:L.361, A:L.437 OLC.12: 4 residues within 4Å: Chain A: P.299, T.300 Chain B: L.37, A.42 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.299 OLC.13: 1 residues within 4Å: Chain A: H.149 No protein-ligand interaction detected (PLIP) OLC.14: 1 residues within 4Å: Chain A: V.33 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.33 OLC.16: 5 residues within 4Å: Chain B: V.28, L.32, Y.35 Chain C: Y.27, F.31 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.28, B:L.32, B:Y.35 Hydrogen bonds: B:Y.35 OLC.17: 6 residues within 4Å: Chain A: P.365, H.447 Chain C: F.22, G.25, A.32 Ligands: OLC.18 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:P.365, A:H.447, C:F.22 OLC.18: 4 residues within 4Å: Chain A: W.448, L.451 Chain C: R.33 Ligands: OLC.17 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:R.33, C:R.33 Salt bridges: C:R.33 Hydrophobic interactions: A:W.448 OLC.19: 6 residues within 4Å: Chain B: A.13, Y.14, F.21 Chain C: I.12, L.13, T.16 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:I.12, C:L.13, C:T.16, B:Y.14, B:Y.14, B:F.21, B:F.21

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

CUA.15: 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

Andersson, R. et al., Serial femtosecond crystallography structure of cytochrome c oxidase at room temperature. Sci Rep (2017)

Release Date

2017-08-23

Peptides

Cytochrome c oxidase subunit 1: A
Cytochrome c oxidase subunit 2: B
Cytochrome c oxidase polypeptide IIA: 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 IIA

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