SMTL ID : 9gdf.1

Chloride bound structure of oxidized ba3-type cytochrome c oxidase confirmed by single-wavelength anomalous diffraction

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

CU.1: 4 residues within 4Å: Chain A: H.240, H.289, H.290 Ligands: CL.17 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, 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 24 PLIP interactions: 24 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: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: 34 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, L.327, W.342, V.357, L.360, F.363, G.367, G.370, N.373, A.374, D.379, H.383, V.388, H.391, F.392, Q.395, V.396, R.456 Chain C: V.11 Ligands: CL.16, CL.17 35 PLIP interactions: 34 interactions with chain A, 1 interactions with chain C, 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:L.327, A:W.342, A:V.357, A:L.360, 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 Hydrogen bonds: A:Y.244, A:Y.244 Water bridges: A:H.290, A:N.384, A:N.384 Salt bridges: A:H.383, A:R.456, A:R.457 pi-Cation interactions: A:H.240 Metal complexes: A:H.391

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

OLC.4: 6 residues within 4Å: Chain A: W.348, V.354, L.429, W.433, L.437 Ligands: OLC.8 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.433, A:W.433, A:L.437 OLC.5: 4 residues within 4Å: Chain A: K.147, W.150, S.219, F.220 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.150, A:W.150, 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 Hydrophobic interactions: A:W.118 Hydrogen bonds: A:K.26 OLC.7: 6 residues within 4Å: Chain A: Y.168, L.171, W.174, R.175, G.535, F.538 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.168, A:L.171 Hydrogen bonds: A:R.175 Water bridges: A:G.535 Salt bridges: A:R.175 OLC.8: 5 residues within 4Å: Chain A: A.471, V.472, V.475 Ligands: OLC.4, OLC.9 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.472 OLC.9: 2 residues within 4Å: Chain A: V.478 Ligands: OLC.8 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.478 OLC.10: 3 residues within 4Å: Chain A: L.216, L.222, V.223 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.216 OLC.11: 5 residues within 4Å: Chain A: R.344, W.348, L.361, F.436, L.437 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.348, A:L.361, A:F.436, A:L.437 OLC.12: 3 residues within 4Å: Chain A: L.129, H.149, A.151 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.129, A:A.151 OLC.13: 6 residues within 4Å: Chain A: Y.30, V.33, L.34, L.37, W.117, F.121 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.30, A:V.33, A:L.34, A:L.37, A:W.117, A:F.121 OLC.14: 11 residues within 4Å: Chain A: P.365, V.444, H.447, L.451 Chain C: V.21, F.22, G.25, A.28, V.29, A.32 Ligands: OLC.15 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:P.365, A:H.447, A:L.451, C:F.22 Water bridges: C:A.32 OLC.15: 5 residues within 4Å: Chain A: W.448, L.451 Chain C: V.29, R.33 Ligands: OLC.14 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:R.33 Salt bridges: C:R.33 Hydrophobic interactions: A:W.448 OLC.18: 9 residues within 4Å: Chain A: P.299, T.300, M.303, I.304, L.308 Chain B: L.37, A.42, I.45, P.46 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.37, A:P.299, A:M.303, A:I.304, A:L.308 OLC.20: 5 residues within 4Å: Chain B: V.28, L.32, Y.35 Chain C: Y.27, F.31 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:V.28, B:L.32, B:Y.35, B:Y.35 Hydrogen bonds: B:Y.35, C:Y.27 OLC.21: 8 residues within 4Å: Chain B: A.13, Y.14, G.17, W.18, F.21 Chain C: I.12, L.13, T.16 9 PLIP interactions: 3 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:I.12, C:L.13, C:T.16, B:Y.14, B:F.21, B:F.21 Hydrogen bonds: B:Y.14, B:Y.14, B:G.17

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.16: 5 residues within 4Å: Chain A: Y.244, L.247, S.316, F.363 Ligands: HAS.3 Ligand excluded by PLIP CL.17: 6 residues within 4Å: Chain A: H.240, V.243, H.289, H.290 Ligands: CU.1, HAS.3 Ligand excluded by PLIP

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

CUA.19: 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

Zoric, D. et al., Structural changes in cytochrome c oxidase following the reduction of dioxygen to water. To Be Published

Release Date

2025-08-13

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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