SMTL ID : 8qh4.1 (1 other biounit)

Crystal structure of reduced respiratory Complex I subunits NuoEF from Aquifex aeolicus bound to oxidized 3-acetylpyridine adenine dinucleotide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.96 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

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

SO4.2: 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 SO4.3: 4 residues within 4Å: Chain A: F.73, D.74, R.75, E.76 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.75, A:E.76 Salt bridges: A:R.75 SO4.8: 2 residues within 4Å: Chain B: V.81, R.87 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.87, B:R.87, B:R.87 Salt bridges: B:R.87

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 FNR: 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL(Non-covalent)

FNR.5: 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: A3D.6 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:Y.180, B:Y.180, B:I.181, B:E.184, B:E.184, B:L.395 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, B:T.223 Water bridges: B:G.67, B:N.92, B:E.95, B:Y.180, B:G.183 Salt bridges: B:K.76

1 x A3D: 3-ACETYLPYRIDINE ADENINE DINUCLEOTIDE(Non-covalent)

A3D.6: 12 residues within 4Å: Chain B: G.68, A.69, F.71, K.76, E.185, K.202, Y.205, P.206, V.207, L.297 Ligands: FNR.5, NA.9 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:G.68, B:K.76, B:K.76, B:E.185 Water bridges: B:A.69, B:E.97, B:Y.180, B:Y.180, B:K.202, B:Y.205, B:Y.205 Salt bridges: B:K.202, B:K.202 pi-Stacking: B:F.71, B:Y.205, B:Y.205

1 x GOL: GLYCEROL(Non-functional Binders)

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

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

NA.9: 3 residues within 4Å: Chain B: E.97, T.319 Ligands: A3D.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.319 Water bridges: B:E.97, B:T.319 NA.10: 1 residues within 4Å: Chain B: E.52 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.52 NA.11: 2 residues within 4Å: Chain B: E.150, K.154 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.150, B:E.150 NA.12: 2 residues within 4Å: Chain B: D.94, A.179 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.94, B:A.179 Water bridges: B:S.96, B:A.177, B:G.178 NA.13: 4 residues within 4Å: Chain A: D.71, Q.126 Chain B: G.178, E.345 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.71, A:D.71

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wohlwend, D. et al., Structures of 3-acetylpyridine adenine dinucleotide and ADP-ribose bound to the electron input module of respiratory complex I. Structure (2024)

Release Date

2024-04-03

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NADH-quinone oxidoreductase subunit E

NADH-quinone oxidoreductase subunit F

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