SMTL ID : 8evu.1

Cryo EM structure of Vibrio cholerae NQR

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-mer

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Covalent)

FMN.1: 19 residues within 4Å: Chain B: I.169, R.209, F.213, W.226, T.236, A.237, L.238, S.239, S.271, E.274, G.334, G.335, M.343, P.379, E.380, G.381, M.382, M.383, L.384 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:I.169, B:E.274, B:M.382, B:M.383 Hydrogen bonds: B:L.238, B:S.239, B:S.271, B:E.274, B:G.335, B:E.380, B:E.380, B:E.380, B:M.382, B:M.383, B:L.384 pi-Cation interactions: B:R.209 FMN.4: 18 residues within 4Å: Chain B: F.213, F.214, P.217, S.221, G.222, D.223, A.377 Chain C: L.145, W.146, E.172, T.173, L.176, K.207, G.223, A.224, T.225, L.226, T.227 16 PLIP interactions: 11 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:W.146, B:F.213, B:F.214, B:P.217 Hydrogen bonds: C:E.172, C:T.173, C:T.173, C:G.223, C:T.225, C:L.226, C:T.227, C:T.227, C:T.227, B:G.222, B:D.223 Salt bridges: C:K.207

1 x RBF: RIBOFLAVIN(Non-covalent)

RBF.2: 20 residues within 4Å: Chain B: I.56, M.57, V.60, G.158, V.161, T.162, L.165, T.197, G.198, N.200, N.203, P.204, A.205, I.292, F.342, M.343, T.345, D.346, P.347, V.348 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:I.56, B:V.60, B:I.292 Hydrogen bonds: B:T.162, B:T.162, B:G.196, B:G.198, B:N.200, B:N.203, B:N.203, B:A.205, B:D.346

1 x UQ1: UBIQUINONE-1(Non-covalent)

UQ1.3: 12 residues within 4Å: Chain A: W.337 Chain B: A.29, L.33, K.54, M.57, I.58, V.155, N.156, E.157, G.158, F.159, F.160 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:A.29, B:V.155, B:F.159, B:F.160, B:F.160, B:F.160 Hydrogen bonds: B:G.158, B:F.159, B:F.160

1 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.5: 8 residues within 4Å: Chain D: G.27, V.28, C.29, C.112 Chain E: G.24, C.26, N.119, C.120 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain E, Metal complexes: D:C.29, D:C.112, E:C.26, E:C.120

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Juarez, O. et al., Novel cofactor binding motifs, electron transfer and ion pumping mechanisms of the respiratory complex NQR. To Be Published

Release Date

2022-11-16

Peptides

Na(+)-translocating NADH-quinone reductase subunit A: A
Na(+)-translocating NADH-quinone reductase subunit B: B
Na(+)-translocating NADH-quinone reductase subunit C: C
Na(+)-translocating NADH-quinone reductase subunit D: D
Na(+)-translocating NADH-quinone reductase subunit E: E
Na(+)-translocating NADH-quinone reductase subunit F: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Membrane

We predict this structure to be a membrane protein.
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Na(+)-translocating NADH-quinone reductase subunit A

Na(+)-translocating NADH-quinone reductase subunit B

Na(+)-translocating NADH-quinone reductase subunit C

Na(+)-translocating NADH-quinone reductase subunit D

Na(+)-translocating NADH-quinone reductase subunit E

Na(+)-translocating NADH-quinone reductase subunit F

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