SMTL ID : 8qgw.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 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.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 FES.10: 10 residues within 4Å: Chain C: 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 C, Metal complexes: C:C.86, C:C.91, C:C.127, C:C.131

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

SO4.2: 2 residues within 4Å: Chain A: K.25, R.27 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.25 Salt bridges: A:K.25, A:R.27 SO4.3: 5 residues within 4Å: Chain A: V.67, 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 SO4.11: 2 residues within 4Å: Chain C: K.25, R.27 3 PLIP interactions: 3 interactions with chain C Water bridges: C:K.25 Salt bridges: C:K.25, C:R.27 SO4.12: 5 residues within 4Å: Chain C: V.67, F.73, D.74, R.75, E.76 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:F.73, C:D.74, C:R.75 Salt bridges: C:R.75 SO4.20: 4 residues within 4Å: Chain D: G.159, K.160, E.170 Ligands: NA.25 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.160

2 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 SF4.14: 13 residues within 4Å: Chain D: 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 D, Metal complexes: D:C.347, D:C.350, D:C.353, D:C.393

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.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 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, 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:N.92, B:E.95, B:G.183 Salt bridges: B:K.76 FMN.15: 20 residues within 4Å: Chain D: 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.16 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:Y.180, D:Y.180, D:I.181, D:E.184, D:E.184, D:L.395 Hydrogen bonds: D:R.66, D:G.67, D:N.92, D:S.96, D:G.183, D:E.185, D:N.219, D:N.220, D:N.220 Water bridges: D:N.92, D:D.94, D:E.95, D:Y.180, D:G.183 Salt bridges: D:K.76

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

A3D.6: 13 residues within 4Å: Chain B: G.68, A.69, F.71, K.76, Y.180, E.185, K.202, Y.205, P.206, V.207, L.297, V.398 Ligands: FMN.5 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:G.68, B:K.76, B:Y.180, B:E.185 Water bridges: B:E.97, B:E.184, 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 A3D.16: 16 residues within 4Å: Chain D: G.68, A.69, F.71, K.76, F.79, Y.180, E.185, K.202, Y.205, P.206, V.207, L.297, Y.342, G.394, V.398 Ligands: FMN.15 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:Y.180, D:V.398 Hydrogen bonds: D:G.68, D:K.76, D:Y.180, D:E.185 Water bridges: D:Y.180, D:E.184, D:G.394 Salt bridges: D:K.202, D:K.202 pi-Stacking: D:F.71, D:Y.205, D:Y.205

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 8 residues within 4Å: Chain B: Y.34, D.37, G.38, G.39, E.116, P.228, F.229, S.232 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:E.116, B:S.232, B:S.232 Water bridges: B:R.22, B:D.37, B:G.39, B:Y.40, B:Y.40 GOL.17: 7 residues within 4Å: Chain D: Y.34, D.37, G.38, G.39, E.116, P.228, F.229 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:E.116, D:S.232, D:S.232 Water bridges: D:R.22, D:D.37, D:Y.40, D:Y.40 GOL.18: 5 residues within 4Å: Chain B: G.159, K.160, E.170 Chain D: K.25, R.27 8 PLIP interactions: 3 interactions with chain D, 5 interactions with chain B Hydrogen bonds: D:K.25, D:R.27, B:K.160, B:K.160, B:K.160, B:E.170, B:E.170 Water bridges: D:E.33 GOL.19: 1 residues within 4Å: Chain D: R.87 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:R.87, D:R.87 Water bridges: D:E.52, D:E.52, D:I.125, D:G.126

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 1 residues within 4Å: Chain B: R.87 Ligand excluded by PLIP

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

NA.9: 5 residues within 4Å: Chain B: I.7, R.104, I.105, E.108, R.109 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.108, B:E.108, B:R.109 NA.13: 2 residues within 4Å: Chain C: V.87, P.124 No protein-ligand interaction detected (PLIP) NA.21: 5 residues within 4Å: Chain D: I.7, R.104, I.105, E.108, R.109 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.108, D:R.109 NA.22: 2 residues within 4Å: Chain C: P.24 Chain D: E.129 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.129 NA.23: 1 residues within 4Å: Chain D: E.151 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.151 Water bridges: D:I.31 NA.24: 5 residues within 4Å: Chain D: K.153, L.158, G.159, L.169, E.170 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.153, D:L.169 Water bridges: D:E.170 NA.25: 3 residues within 4Å: Chain D: K.160, E.170 Ligands: SO4.20 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.170 NA.26: 2 residues within 4Å: Chain D: Q.41, E.44 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.41, D:E.44

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: 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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