SMTL ID : 6saq.2 (1 other biounit)

wild-type NuoEF from Aquifex aeolicus bound to NADH-OH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

hetero-1-1-mer

Ligands

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

FES.1: 10 residues within 4Å: Chain A: C.86, S.88, V.90, C.91, C.127, L.128, G.129, A.130, C.131, V.136 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.86, A:C.91, A:C.127, A:C.131

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 20 residues within 4Å: Chain B: G.65, R.66, G.67, K.76, N.92, D.94, E.95, S.96, Y.180, I.181, G.183, E.184, E.185, V.218, N.219, N.220, T.223, G.394, L.395 Ligands: L3W.4 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:Y.180, B:Y.180, B:I.181, B:E.184, B:E.184 Hydrogen bonds: B:R.66, B:G.67, B:N.92, B:S.96, B:G.183, B:E.185, B:N.219, B:N.220, B:N.220 Water bridges: B:G.67, B:N.92, B:D.94, B:E.95, B:G.183 Salt bridges: B:K.76

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.3: 13 residues within 4Å: Chain B: I.181, P.199, T.346, C.347, G.348, Q.349, C.350, C.353, S.391, I.392, C.393, L.395, G.396 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.347, B:C.350, B:C.353, B:C.393

1 x L3W: [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-[[(1~{E},3~{Z})-5-azanyl-4-oxidanyl-5-oxidanylidene-penta-1,3-dienyl]-methanoyl-amino]-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate(Non-covalent)

L3W.4: 20 residues within 4Å: Chain B: G.67, G.68, A.69, F.71, K.76, F.79, E.95, S.96, E.97, T.100, D.103, Y.180, E.185, Y.205, P.206, V.207, N.220, L.297, T.319 Ligands: FMN.2 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:E.97, B:T.319 Hydrogen bonds: B:G.67, B:K.76, B:E.95, B:E.95, B:S.96, B:E.97, B:E.185, B:N.220 Water bridges: B:E.95, B:E.184, B:E.184, B:Y.205, B:G.394 pi-Stacking: B:F.71, B:Y.205, B:Y.205

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain B: P.267, T.270, E.274, K.278, Y.279 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.278, B:K.278 Water bridges: B:N.269 GOL.6: 7 residues within 4Å: Chain B: R.22, Y.34, L.113, E.116, P.228, F.229, S.232 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.22, B:R.22, B:Y.34, B:E.116, B:S.232, B:S.232 Water bridges: B:Y.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Friedrich, T. et al., Structural Basis for Inhibition of ROS-Producing Respiratory Complex I by NADH-OH. Angew.Chem.Int.Ed.Engl. (2021)

Release Date

2020-07-22

Peptides

NADH-quinone oxidoreductase subunit E: A
NADH-quinone oxidoreductase subunit F: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

NADH-quinone oxidoreductase subunit E

NADH-quinone oxidoreductase subunit F

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