SMTL ID : 6e2a.1

Crystal structure of NADH:quinone reductase PA1024 from Pseudomonas aeruginosa PAO1 in complex with NAD+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 23 residues within 4Å: Chain A: G.21, G.22, M.23, Q.24, N.73, T.75, A.103, K.124, D.145, C.149, A.150, S.178, G.179, G.180, N.199, M.200, G.201, T.202, L.205, Y.277, S.288, V.292 Ligands: NAD.2 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:M.23, A:L.205 Hydrogen bonds: A:G.22, A:Q.24, A:N.73, A:T.75, A:K.124, A:K.124, A:A.150, A:S.178, A:G.180, A:N.199, A:G.201, A:T.202, A:T.202 Water bridges: A:G.179, A:G.179, A:R.203 FMN.5: 23 residues within 4Å: Chain B: G.21, G.22, M.23, Q.24, N.73, T.75, A.103, K.124, D.145, C.149, A.150, S.178, G.179, G.180, N.199, M.200, G.201, T.202, L.205, Y.277, S.288, V.292 Ligands: NAD.6 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:M.23, B:L.205 Hydrogen bonds: B:G.22, B:Q.24, B:N.73, B:T.75, B:T.75, B:K.124, B:K.124, B:A.150, B:S.178, B:G.180, B:N.199, B:G.201, B:T.202 Water bridges: B:D.145, B:G.179, B:G.179, B:R.203

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.2: 15 residues within 4Å: Chain A: Q.24, W.25, L.77, P.78, T.79, Q.80, G.151, H.152, M.232, N.237, Y.261, V.268, G.270, S.288 Ligands: FMN.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Q.24 Hydrogen bonds: A:L.77, A:Q.80, A:H.152, A:G.270, A:S.288, A:S.288 Water bridges: A:L.77, A:G.151 pi-Stacking: A:Y.261, A:Y.261 NAD.6: 15 residues within 4Å: Chain B: Q.24, W.25, L.77, P.78, T.79, Q.80, G.151, H.152, M.232, N.237, Y.261, V.268, G.270, S.288 Ligands: FMN.5 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Q.24 Hydrogen bonds: B:L.77, B:Q.80, B:H.152, B:Y.261, B:G.270, B:S.288, B:S.288 Water bridges: B:T.75, B:L.77, B:G.151 pi-Stacking: B:Y.261, B:Y.261

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: D.156, I.158 Chain B: E.225, R.226, S.227, T.228, R.240, M.291 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:D.156, B:E.225, B:T.228, B:R.240 Water bridges: A:D.157, B:D.229, B:L.230, B:R.243 GOL.4: 2 residues within 4Å: Chain A: R.221, D.297 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.221, A:D.297 GOL.7: 8 residues within 4Å: Chain A: E.225, R.226, S.227, T.228, R.240, M.291 Chain B: D.156, I.158 7 PLIP interactions: 1 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:D.156, A:E.225, A:T.228, A:R.240 Water bridges: A:D.229, A:D.229, A:L.230 GOL.8: 2 residues within 4Å: Chain B: R.221, D.297 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.221, B:D.297

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ball, J. et al., Steric hindrance controls pyridine nucleotide specificity of a flavin-dependent NADH:quinone oxidoreductase. Protein Sci. (2019)

Release Date

2019-02-06

Peptides

Nitronate monooxygenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Nitronate monooxygenase