SMTL ID : 7xmd.1

Cryo-EM structure of Cytochrome bo3 from Escherichia coli, the structure complexed with an allosteric inhibitor N4

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x HEO: HEME O(Non-covalent)

HEO.1: 37 residues within 4Å: Chain A: W.170, W.280, V.287, Y.288, I.291, H.333, H.334, T.352, A.356, T.359, G.360, I.363, F.391, S.392, G.395, G.398, V.399, L.401, A.402, D.407, H.411, N.412, L.416, H.419, F.420, V.423, I.424, V.428, R.481 Chain B: M.51, V.54, V.55, A.58, P.96, I.99, I.100 Ligands: CU.3 32 PLIP interactions: 27 interactions with chain A, 5 interactions with chain B, Hydrophobic interactions: A:W.280, A:V.287, A:V.287, A:I.291, A:I.291, A:H.334, A:T.352, A:A.356, A:T.359, A:I.363, A:F.391, A:L.401, A:L.416, A:L.416, A:F.420, A:F.420, A:V.423, A:I.424, A:V.428, B:V.55, B:A.58, B:P.96, B:I.99, B:I.100 Hydrogen bonds: A:Y.288, A:D.407 Salt bridges: A:H.411, A:R.481 pi-Stacking: A:H.333 pi-Cation interactions: A:H.284, A:H.284 Metal complexes: A:H.419

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

HEM.2: 25 residues within 4Å: Chain A: F.73, A.76, M.79, R.80, Q.83, Y.99, F.103, H.106, G.107, M.110, I.111, A.115, G.169, W.170, I.417, F.420, H.421, I.424, I.425, V.429, W.460, F.468, R.481, R.482, I.505 25 PLIP interactions: 25 interactions with chain A, Hydrophobic interactions: A:F.73, A:A.76, A:M.110, A:I.111, A:A.115, A:W.170, A:W.170, A:I.417, A:F.420, A:I.424, A:I.425, A:V.429, A:W.460, A:I.505 Hydrogen bonds: A:Q.83, A:Q.83, A:Y.99, A:F.103, A:W.170, A:R.482 Salt bridges: A:R.481, A:R.482 pi-Stacking: A:F.420 Metal complexes: A:H.106, A:H.421

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

CU.3: 4 residues within 4Å: Chain A: H.284, H.333, H.334 Ligands: HEO.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.284, A:H.333, A:H.334

2 x PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine(Non-covalent)

PEE.4: 22 residues within 4Å: Chain A: A.137, F.138, P.139, F.140, L.141, L.144, F.148, W.192, I.199, L.203, T.247, F.602, F.618, M.621, W.625, K.628, V.634 Chain C: K.25, G.28, F.29, Y.32 Ligands: PEE.7 26 PLIP interactions: 4 interactions with chain C, 22 interactions with chain A Hydrophobic interactions: C:Y.32, C:Y.32, A:F.138, A:F.138, A:L.141, A:L.141, A:L.144, A:F.148, A:W.192, A:I.199, A:L.203, A:T.247, A:F.602, A:F.602, A:F.618, A:W.625, A:W.625, A:W.625, A:W.625 Salt bridges: C:K.25, C:K.25 Hydrogen bonds: A:A.137, A:F.140, A:L.141, A:K.628, A:K.628 PEE.7: 18 residues within 4Å: Chain A: I.622, W.625, I.626, K.628, S.629 Chain C: K.25, F.29, Y.32, T.145, L.148, H.149, T.151, S.152, I.155, W.156, R.176, F.183 Ligands: PEE.4 17 PLIP interactions: 7 interactions with chain A, 10 interactions with chain C Hydrophobic interactions: A:I.622, A:W.625, A:W.625, A:W.625, A:I.626, C:F.29, C:T.145, C:L.148, C:L.148, C:T.151, C:W.156, C:W.156, C:F.183 Hydrogen bonds: A:K.628, A:S.629 Salt bridges: C:K.25, C:R.176

1 x JYR: methyl 3-oxidanyl-5-[oxidanyl(oxidanylidene)-$l^{4}-azanyl]-1-benzothiophene-2-carboxylate(Non-covalent)

JYR.5: 11 residues within 4Å: Chain A: M.18, I.21, R.71, A.74, D.75, M.78, Q.101, I.102, A.105, L.160, F.165 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.21, A:I.21, A:R.71, A:L.160 Hydrogen bonds: A:R.71, A:R.71 Salt bridges: A:R.71

1 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.6: 4 residues within 4Å: Chain A: M.273 Chain B: M.186, M.189 Chain D: M.106 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nishida, Y. et al., Identifying antibiotics based on structural differences in the conserved allostery from mitochondrial heme-copper oxidases. Nat Commun (2022)

Release Date

2022-12-21

Peptides

Cytochrome bo(3) ubiquinol oxidase subunit 1: A
Ubiquinol oxidase subunit 2: B
Cytochrome bo(3) ubiquinol oxidase subunit 3: C
Cytochrome bo(3) ubiquinol oxidase subunit 4: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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Cytochrome bo(3) ubiquinol oxidase subunit 1

Ubiquinol oxidase subunit 2

Cytochrome bo(3) ubiquinol oxidase subunit 3

Cytochrome bo(3) ubiquinol oxidase subunit 4

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