SMTL ID : 6rx4.1

THE STRUCTURE OF BD OXIDASE FROM ESCHERICHIA COLI

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

2 x HEB: HEME B/C(Non-covalent)

HEB.1: 20 residues within 4Å: Chain A: Q.152, K.183, H.186, T.187, S.190, V.234, G.238, S.241, M.245, K.252, M.393, V.394, G.397, F.398, P.433, A.436, V.437, G.440, W.441, A.444 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:V.234, A:V.394, A:F.398, A:A.436, A:V.437, A:V.437, A:W.441, A:W.441, A:A.444 Hydrogen bonds: A:Q.152 Salt bridges: A:K.183, A:K.183, A:K.252 Metal complexes: A:H.186 HEB.2: 20 residues within 4Å: Chain A: R.9, F.12, A.13, A.16, M.17, F.20, F.77, W.81, Y.84, F.92, I.144, N.148, M.151, W.441, E.445, R.448, Q.449, A.452, T.459 Ligands: HDD.3 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:R.9, A:F.12, A:F.12, A:A.13, A:F.20, A:F.77, A:W.81, A:Y.84, A:F.92, A:I.144, A:W.441, A:W.441, A:W.441, A:E.445, A:A.452 Hydrogen bonds: A:Q.449, A:T.459 Salt bridges: A:R.9, A:R.448 pi-Cation interactions: A:R.448

1 x HDD: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE(Non-covalent)

HDD.3: 21 residues within 4Å: Chain A: H.19, F.20, V.23, T.26, F.63, G.66, V.67, G.70, M.73, E.74, F.77, F.104, E.107, S.108, S.140, A.141, I.144, L.145 Chain B: V.62, I.65 Ligands: HEB.2 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:V.23, A:V.23, A:T.26, A:M.73, A:F.77, A:F.104, A:F.104, A:F.104, A:A.141, A:I.144, A:I.144, A:L.145, B:I.65 Hydrogen bonds: A:S.108, A:S.140 Metal complexes: A:H.19

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

PEE.4: 14 residues within 4Å: Chain B: G.21, T.25, Y.187, M.190, R.191, A.289, F.292, S.296, L.297, A.300, Y.359, F.363, G.364, R.365 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:T.25, B:Y.187, B:L.297, B:A.300, B:F.363 Salt bridges: B:R.191, B:R.365, B:R.365

1 x UQ8: Ubiquinone-8(Non-covalent)

UQ8.5: 29 residues within 4Å: Chain B: W.12, G.16, L.19, F.22, A.23, L.64, L.71, V.78, A.82, I.134, G.135, A.137, F.138, L.141, L.142, A.172, F.215, A.218, G.219, V.222, L.256, F.259, P.269, I.303, T.305, G.307, A.309, M.310, V.314 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:W.12, B:L.19, B:F.22, B:A.23, B:L.64, B:L.71, B:V.78, B:A.82, B:I.134, B:I.134, B:A.137, B:F.138, B:F.138, B:F.138, B:F.138, B:L.141, B:L.142, B:L.142, B:A.218, B:V.222, B:I.303, B:I.303, B:I.303, B:A.309, B:V.314

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thesseling, A. et al., Homologous bd oxidases share the same architecture but differ in mechanism. Nat Commun (2019)

Release Date

2019-11-20

Peptides

Cytochrome bd-I ubiquinol oxidase subunit 1: A
Cytochrome bd-I ubiquinol oxidase subunit 2: B
Cytochrome bd-I ubiquinol oxidase subunit X: C
Cytochrome bd-I ubiquinol oxidase subunit Y: 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 bd-I ubiquinol oxidase subunit 1

Cytochrome bd-I ubiquinol oxidase subunit 2

Cytochrome bd-I ubiquinol oxidase subunit X

Cytochrome bd-I ubiquinol oxidase subunit Y

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