SMTL ID : 8k65.1

Serial femtosecond crystallography structure of CO bound ba3- type cytochrome c oxidase without pump laser irradiation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 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: CMO.14 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.240, A:H.289, A:H.290, CMO.14

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 27 PLIP interactions: 27 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: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.53, A:Y.140, A:R.456, A:R.456 Salt bridges: A:R.456, A:R.457 pi-Stacking: A:F.392 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, H.289, H.290, T.309, S.316, L.317, A.320, 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 Chain C: V.11 Ligands: CMO.14 37 PLIP interactions: 34 interactions with chain A, 2 interactions with chain C, 1 Ligand-Ligand 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:V.357, A:L.360, A:L.361, A:F.363, A:F.363, A:I.364, 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:V.11 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 pi-Cation interactions: A:H.240, A:H.240 Metal complexes: A:H.391, CMO.14

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

OLC.4: 4 residues within 4Å: Chain A: W.348, V.354, W.433, L.437 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.433, A:W.433, A:L.437 OLC.5: 5 residues within 4Å: Chain A: K.147, W.150, S.219, F.220, G.221 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: 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: 3 residues within 4Å: Chain A: W.164, F.201, F.538 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.201, A:F.538 OLC.8: 2 residues within 4Å: Chain A: V.475 Ligands: OLC.9 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.475 OLC.9: 3 residues within 4Å: Chain A: V.56, V.478 Ligands: OLC.8 No protein-ligand interaction detected (PLIP) OLC.10: 4 residues within 4Å: Chain A: V.212, L.216, L.222, V.223 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.216 OLC.11: 4 residues within 4Å: Chain A: R.344, W.348, W.433, L.437 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.348, A:W.348, A:W.348, A:W.433 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: 3 residues within 4Å: Chain A: Y.30, L.34, L.37 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.30, A:L.37 OLC.15: 3 residues within 4Å: Chain A: P.299 Chain B: L.37, A.42 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.299 OLC.17: 5 residues within 4Å: Chain B: V.28, L.32, Y.35 Chain C: Y.27, F.31 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.28, B:Y.35 OLC.18: 7 residues within 4Å: Chain B: A.13, Y.14, G.17, F.21 Chain C: I.12, L.13, L.17 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:I.12, C:L.13, C:L.17, B:Y.14, B:Y.14, B:F.21, B:F.21, B:F.21 OLC.19: 8 residues within 4Å: Chain A: P.365, H.447 Chain C: V.21, F.22, G.25, A.28, A.32 Ligands: OLC.20 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:F.22, A:P.365 OLC.20: 5 residues within 4Å: Chain A: W.448, L.451 Chain C: A.32, R.33 Ligands: OLC.19 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

1 x CMO: CARBON MONOXIDE(Non-functional Binders)

CMO.14: 5 residues within 4Å: Chain A: H.240, V.243, H.290 Ligands: CU.1, HAS.3 No protein-ligand interaction detected (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

Safari, C. et al., Time-resolved serial crystallography to track the dynamics of carbon monoxide in the active site of cytochrome c oxidase. Sci Adv (2023)

Release Date

2023-11-15

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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