SMTL ID : 8qg1.1

Crystal structure of oxidized respiratory Complex I subunits NuoEF from Aquifex aeolicus bound to ADP-ribose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 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.11: 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: 5 residues within 4Å: Chain A: V.67, F.73, D.74, R.75, E.76 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.67, A:R.75, A:E.76 Salt bridges: A:R.75 SO4.3: 3 residues within 4Å: Chain A: K.25, R.27 Ligands: CL.4 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.25, A:R.27 SO4.9: 1 residues within 4Å: Chain B: R.87 3 PLIP interactions: 3 interactions with chain B Water bridges: B:V.81, B:R.87 Salt bridges: B:R.87 SO4.12: 4 residues within 4Å: Chain C: V.67, F.73, D.74, R.75 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.74, C:D.74, C:R.75 Water bridges: C:R.75 SO4.13: 2 residues within 4Å: Chain C: K.25, R.27 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:K.25, C:R.27

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

CL.4: 3 residues within 4Å: Chain A: K.25, K.26 Ligands: SO4.3 Ligand excluded by PLIP

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

SF4.5: 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.6: 19 residues within 4Å: Chain B: G.65, R.66, G.67, K.76, N.92, D.94, E.95, Y.180, I.181, G.183, E.184, E.185, V.218, N.219, N.220, T.223, G.394, L.395 Ligands: APR.7 23 PLIP interactions: 23 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.65, B:G.65, B:N.92, B:E.95, B:E.97, B:G.183 Salt bridges: B:K.76 FMN.15: 19 residues within 4Å: Chain D: G.65, R.66, G.67, K.76, N.92, D.94, E.95, Y.180, I.181, G.183, E.184, E.185, V.218, N.219, N.220, T.223, G.394, L.395 Ligands: APR.16 22 PLIP interactions: 22 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:G.70, D:D.94, D:D.94, D:E.95, D:Y.180, D:G.183 Salt bridges: D:K.76

2 x APR: ADENOSINE-5-DIPHOSPHORIBOSE(Non-covalent)

APR.7: 10 residues within 4Å: Chain B: G.68, A.69, F.71, K.76, E.185, Y.205, P.206, V.207, L.297 Ligands: FMN.6 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:K.76, B:E.185 Water bridges: B:Y.180, B:E.185, B:K.202, B:Y.205, B:Y.205 pi-Stacking: B:F.71, B:Y.205, B:Y.205 APR.16: 12 residues within 4Å: Chain D: G.68, A.69, F.71, K.76, F.79, E.185, K.202, Y.205, P.206, V.207, L.297 Ligands: FMN.15 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:K.76, D:E.185 Water bridges: D:F.71, D:E.184 Salt bridges: D:K.202, D:K.202 pi-Stacking: D:F.71, D:Y.205, D:Y.205

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 9 residues within 4Å: Chain B: Y.34, D.37, G.38, G.39, A.42, E.116, P.228, F.229, S.232 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.38, B:Y.40, B:E.116, B:S.232 Water bridges: B:R.22, B:A.42, B:S.232 GOL.19: 1 residues within 4Å: Chain D: K.288 1 PLIP interactions: 1 interactions with chain D Water bridges: D:E.327 GOL.20: 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:A.42

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

NA.10: 2 residues within 4Å: Chain B: E.53, W.57 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.53, B:W.57 NA.21: 3 residues within 4Å: Chain D: M.49, S.50, E.53 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.50, D:E.53, D:E.53

2 x MPO: 3[N-MORPHOLINO]PROPANE SULFONIC ACID(Non-covalent)

MPO.17: 3 residues within 4Å: Chain D: G.159, K.160, E.170 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.160 Salt bridges: D:K.160 MPO.18: 5 residues within 4Å: Chain B: G.159, K.160, E.170 Chain D: K.25, R.27 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain B Salt bridges: D:K.25, D:R.27, B:K.160 Hydrogen bonds: B:K.160, B:E.170

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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