SMTL ID : 6q9k.2 (2 other biounits)

Crystal structure of reduced Aquifex aeolicus NADH-quinone oxidoreductase subunits NuoE and NuoF S96M bound to NADH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

hetero-2-2-mer

Ligands

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

FES.1: 10 residues within 4Å: Chain A: C.81, S.83, V.85, C.86, C.122, L.123, G.124, A.125, C.126, V.131 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.81, A:C.86, A:C.122, A:C.126 FES.12: 9 residues within 4Å: Chain C: C.81, S.83, V.85, C.86, C.122, L.123, G.124, A.125, C.126 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.81, C:C.86, C:C.122, C:C.126

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

SO4.2: 2 residues within 4Å: Chain A: K.20, R.22 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.22 Salt bridges: A:K.20, A:R.22 SO4.3: 4 residues within 4Å: Chain A: F.68, D.69, R.70, E.71 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.70, A:E.71 Salt bridges: A:R.70 SO4.13: 4 residues within 4Å: Chain C: F.68, D.69, R.70, E.71 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:F.68, C:D.69, C:R.70, C:E.71 Salt bridges: C:R.70 SO4.14: 2 residues within 4Å: Chain C: K.20, R.22 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:K.20, C:R.22 SO4.19: 3 residues within 4Å: Chain D: G.158, K.159, E.169 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.159 Salt bridges: D:K.159

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

SF4.4: 13 residues within 4Å: Chain B: I.180, P.198, T.345, C.346, G.347, Q.348, C.349, C.352, S.390, I.391, C.392, L.394, G.395 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.346, B:C.349, B:C.352, B:C.392 SF4.15: 13 residues within 4Å: Chain D: I.180, P.198, T.345, C.346, G.347, Q.348, C.349, C.352, S.390, I.391, C.392, L.394, G.395 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.346, D:C.349, D:C.352, D:C.392

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.5: 20 residues within 4Å: Chain B: G.64, R.65, G.66, K.75, N.91, D.93, E.94, M.95, Y.179, I.180, G.182, E.183, E.184, V.217, N.218, N.219, T.222, G.393, L.394 Ligands: NAI.6 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:Y.179, B:I.180, B:E.183, B:E.183, B:L.394 Hydrogen bonds: B:R.65, B:G.66, B:G.67, B:N.91, B:E.94, B:M.95, B:G.182, B:E.184, B:N.218, B:N.219, B:N.219, B:T.222 Water bridges: B:F.70, B:N.91, B:D.93, B:G.182 Salt bridges: B:K.75 FMN.16: 20 residues within 4Å: Chain D: G.64, R.65, G.66, K.75, N.91, D.93, E.94, M.95, Y.179, I.180, G.182, E.183, E.184, V.217, N.218, N.219, T.222, G.393, L.394 Ligands: NAI.17 23 PLIP interactions: 23 interactions with chain D Hydrophobic interactions: D:Y.179, D:I.180, D:E.183, D:E.183, D:L.394 Hydrogen bonds: D:R.65, D:G.66, D:G.67, D:N.91, D:E.94, D:M.95, D:G.182, D:E.184, D:N.219, D:N.219 Water bridges: D:G.69, D:G.69, D:F.70, D:N.91, D:D.93, D:D.93, D:G.182 Salt bridges: D:K.75

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

NAI.6: 17 residues within 4Å: Chain B: G.66, G.67, A.68, F.70, K.75, F.78, E.94, M.95, E.96, Y.179, E.184, Y.204, P.205, V.206, L.296, T.318 Ligands: FMN.5 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:E.96, B:Y.179 Hydrogen bonds: B:G.66, B:K.75, B:M.95, B:E.96, B:E.184 Water bridges: B:E.184, B:Y.204, B:Y.204, B:Y.204, B:N.219, B:G.393 pi-Stacking: B:F.70, B:Y.204, B:Y.204 NAI.17: 17 residues within 4Å: Chain D: G.66, G.67, A.68, F.70, K.75, F.78, E.94, M.95, E.96, Y.179, E.184, Y.204, P.205, V.206, L.296, T.318 Ligands: FMN.16 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:E.96, D:Y.179 Hydrogen bonds: D:G.66, D:K.75, D:M.95, D:E.96, D:E.184 Water bridges: D:E.94, D:E.184, D:N.219, D:G.393 pi-Stacking: D:F.70, D:Y.204, D:Y.204

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 8 residues within 4Å: Chain B: Y.33, D.36, G.37, G.38, A.41, E.115, P.227, F.228 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.39, B:E.115, B:S.231, B:S.231 Water bridges: B:R.21, B:D.36, B:A.41 GOL.8: 5 residues within 4Å: Chain B: G.158, K.159, E.169 Chain D: K.24, R.26 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain B Hydrogen bonds: D:K.24, D:R.26, B:K.159, B:E.169, B:E.169 Water bridges: D:R.26, B:L.157 GOL.9: 1 residues within 4Å: Chain B: R.86 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.86, B:R.86 GOL.18: 7 residues within 4Å: Chain D: Y.33, D.36, G.37, G.38, E.115, P.227, F.228 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:E.115 Water bridges: D:R.21, D:D.36, D:Y.39, D:A.41, D:S.231, D:S.231

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

NA.10: 2 residues within 4Å: Chain B: V.27, E.32 8 PLIP interactions: 8 interactions with chain B Water bridges: B:R.26, B:V.27, B:S.29, B:S.29, B:S.29, B:E.32, B:E.32, B:E.32 NA.11: 4 residues within 4Å: Chain B: I.6, I.104, E.107, R.108 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.107, B:R.108, B:R.108 NA.20: 2 residues within 4Å: Chain D: E.358, N.361 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.358 NA.21: 2 residues within 4Å: Chain D: P.242, D.309 No protein-ligand interaction detected (PLIP) NA.22: 3 residues within 4Å: Chain D: I.6, E.107, R.108 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.107, D:R.108

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: AC
NADH-quinone oxidoreductase subunit F: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

NADH-quinone oxidoreductase subunit E

NADH-quinone oxidoreductase subunit F

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