SMTL ID : 5weh.2 (1 other biounit)

Cytochrome c oxidase from Rhodobacter sphaeroides in the reduced state

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.45 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

2 x LMU: DODECYL-ALPHA-D-MALTOSIDE(Non-covalent)

LMU.1: 1 residues within 4Å: Chain A: E.69 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.69 LMU.9: 2 residues within 4Å: Chain A: W.451, Y.517 No protein-ligand interaction detected (PLIP)

2 x HEA: HEME-A(Non-covalent)

HEA.2: 35 residues within 4Å: Chain A: L.34, G.37, G.38, G.41, V.45, T.48, M.51, R.52, W.95, I.99, H.102, G.103, M.106, M.107, V.110, V.111, G.171, W.172, Y.414, F.420, H.421, M.424, S.425, V.429, I.432, I.436, M.460, F.468, Q.471, R.481, R.482, A.501, S.504, F.508, F.511 31 PLIP interactions: 31 interactions with chain A, Hydrophobic interactions: A:V.45, A:T.48, A:I.99, A:I.99, A:M.106, A:V.110, A:V.111, A:W.172, A:F.420, A:V.429, A:V.429, A:I.432, A:I.436, A:F.468, A:F.468, A:A.501, A:F.508, A:F.508, A:F.511 Hydrogen bonds: A:T.48, A:T.48, A:R.52, A:W.172, A:Y.414, A:Q.471, A:R.482, A:Y.483 Salt bridges: A:R.481, A:R.481, A:R.482 Metal complexes: A:H.421 HEA.3: 33 residues within 4Å: Chain A: W.172, W.280, V.287, V.291, H.333, H.334, Y.336, T.352, I.355, A.356, T.359, G.360, I.363, F.364, F.391, T.392, G.395, V.396, G.398, I.399, L.401, S.402, D.407, H.411, V.416, H.419, F.420, V.423, M.424, R.481 Chain B: I.43, P.83, I.86 27 PLIP interactions: 24 interactions with chain A, 3 interactions with chain B, Hydrophobic interactions: A:W.280, A:V.287, A:V.291, A:A.356, A:T.359, A:I.363, A:F.364, A:F.391, A:F.391, A:T.392, A:V.396, A:I.399, A:L.401, A:L.401, A:V.416, A:F.420, A:F.420, A:V.423, A:V.423, A:M.424, B:I.43, B:P.83, B:I.86 Salt bridges: A:H.411, A:R.481 pi-Cation interactions: A:H.333 Metal complexes: A:H.419

3 x CU1: COPPER (I) ION(Non-covalent)

CU1.4: 3 residues within 4Å: Chain A: H.284, H.333, H.334 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.284, A:H.333 CU1.10: 6 residues within 4Å: Chain B: H.192, C.227, E.229, C.231, M.238 Ligands: CU1.11 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.192, B:C.227, B:C.231 CU1.11: 6 residues within 4Å: Chain B: C.227, E.229, C.231, H.235, M.238 Ligands: CU1.10 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.231

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 5 residues within 4Å: Chain A: T.337, H.411, D.412 Chain B: D.204, E.229 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Metal complexes: B:E.229, A:H.411, A:D.412

1 x CA: CALCIUM ION(Non-covalent)

CA.6: 6 residues within 4Å: Chain A: E.54, A.57, P.58, G.59, Q.61, D.485 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.54, A:A.57, A:G.59

6 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)

3PE.7: 20 residues within 4Å: Chain A: F.135, P.136, R.137, M.138, L.141, L.145, L.196, L.203 Chain C: H.10, A.25, V.51, M.55, W.58, W.59, V.62, E.65, H.71, G.82, F.86 Ligands: 3PE.12 14 PLIP interactions: 8 interactions with chain C, 6 interactions with chain A Hydrophobic interactions: C:A.25, C:V.51, C:W.58, C:W.58, C:W.59, C:F.86, C:F.86, A:L.196, A:L.203 Hydrogen bonds: C:E.65, A:F.135, A:R.137, A:M.138 Salt bridges: A:R.137 3PE.8: 17 residues within 4Å: Chain A: L.213, R.216, T.221, M.222, H.223, W.237, L.241, V.321 Chain C: M.88 Chain D: Q.19, T.23, G.26, F.27, M.30, V.31, A.34 Ligands: 3PE.15 17 PLIP interactions: 6 interactions with chain D, 11 interactions with chain A Hydrophobic interactions: D:F.27, D:F.27, D:V.31, D:A.34, A:L.213, A:W.237, A:W.237, A:W.237, A:W.237, A:W.237, A:L.241 Hydrogen bonds: D:T.23, D:T.23, A:R.216, A:R.216, A:M.222, A:H.223 3PE.12: 22 residues within 4Å: Chain C: L.52, M.55, W.59, V.62, V.63, S.66, H.71, L.79, F.83, F.86, V.215, I.218, F.219, V.222, R.226, H.231, F.232, K.236, H.237, V.238, G.239 Ligands: 3PE.7 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:L.52, C:W.59, C:W.59, C:W.59, C:W.59, C:F.83, C:F.83, C:F.86, C:V.215, C:I.218, C:F.219, C:F.219, C:V.222 Hydrogen bonds: C:S.66, C:H.231, C:V.238, C:G.239 Salt bridges: C:H.71, C:H.71, C:R.226, C:R.226 3PE.13: 12 residues within 4Å: Chain A: H.277, W.331, Q.344 Chain B: R.209 Chain C: S.95, F.98, W.99, F.102, K.103, Y.107, D.117 Ligands: 3PE.15 10 PLIP interactions: 3 interactions with chain A, 6 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: A:W.331, C:F.98, C:F.98, C:W.99, C:W.99, C:F.102, C:F.102 Hydrogen bonds: A:Q.344, B:R.209 Salt bridges: A:H.277 3PE.14: 3 residues within 4Å: Chain C: I.84, W.245 Chain D: F.24 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.84, C:W.245 Salt bridges: C:H.152 3PE.15: 18 residues within 4Å: Chain A: F.281, V.325, F.328, V.329, S.341, Q.344, Y.347, F.348 Chain C: L.106, Y.107 Chain D: I.38, L.42, L.45, A.46, N.49, A.50 Ligands: 3PE.8, 3PE.13 17 PLIP interactions: 10 interactions with chain A, 7 interactions with chain D Hydrophobic interactions: A:F.281, A:V.325, A:F.328, A:Q.344, A:Y.347, A:Y.347, A:F.348, D:I.38, D:L.42, D:L.45, D:L.45, D:A.46 Hydrogen bonds: A:S.341, A:T.343, A:Q.344, D:A.50, D:A.50

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, J. et al., Role of conformational change and K-path ligands in controlling cytochrome c oxidase activity. Biochem. Soc. Trans. (2017)

Release Date

2017-09-13

Peptides

Cytochrome c oxidase subunit 1: A
Cytochrome c oxidase subunit 2: B
Cytochrome c oxidase polypeptide III (Cytochrome AA3 subunit 3): C
Aa3-type cytochrome c oxidase subunit IV: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
I

D
J

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 III (Cytochrome AA3 subunit 3)

Aa3-type cytochrome c oxidase subunit IV

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