SMTL ID : 6q9g.2 (1 other biounit)

Crystal structure of reduced Aquifex aeolicus NADH-quinone oxidoreductase subunits NuoE G129D and NuoF bound to NADH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 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, D.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

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: F.73, D.74, R.75, E.76 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:F.73, A:D.74, A:R.75, A:E.76, A:E.76 Salt bridges: A:R.75 SO4.3: 2 residues within 4Å: Chain A: K.25, R.27 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.25, A:R.27 SO4.8: 3 residues within 4Å: Chain B: G.159, K.160, E.170 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.160, B:E.170 Salt bridges: B:K.160

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

SF4.4: 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 FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.5: 19 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 Ligands: NAI.6 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:Y.180, B:I.181, B:E.184, B:E.184 Hydrogen bonds: B:R.66, B:G.67, B:G.68, B:N.92, B:E.95, B:S.96, B:G.183, B:E.185, B:N.220, B:N.220 Water bridges: B:G.70, B:G.70, B:F.71, B:N.92, B:D.94, B:D.94, B:G.183 Salt bridges: B:K.76

1 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.6: 17 residues within 4Å: Chain B: G.67, G.68, A.69, F.71, K.76, F.79, E.95, S.96, E.97, Y.180, E.185, Y.205, P.206, V.207, L.297, T.319 Ligands: FMN.5 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:E.97, B:Y.180 Hydrogen bonds: B:G.67, B:K.76, B:S.96, B:E.97, B:E.185, B:V.218 Water bridges: B:E.95, B:E.185, B:N.220 pi-Stacking: B:F.71, B:Y.205, B:Y.205

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 9 residues within 4Å: Chain B: Y.34, D.37, G.38, G.39, L.113, E.116, P.228, F.229, S.232 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.116, B:S.232, B:S.232 Water bridges: B:R.22, B:D.37, B:Y.40, B:A.42

1 x NA: SODIUM ION(Non-functional Binders)

NA.9: 2 residues within 4Å: Chain B: P.243, D.310 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.310

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schulte, M. et al., A mechanism to prevent production of reactive oxygen species by Escherichia coli respiratory complex I. Nat Commun (2019)

Release Date

2019-06-26

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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