SMTL ID : 8au9.1

Xenobiotic reductase A from Pseudomonas putida in complex with 2-methoxyethyl (Z)-2-(hydroxyimino)-3-oxobutanoate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 19 residues within 4Å: Chain A: P.22, P.23, M.24, C.25, A.57, Q.99, H.178, H.181, R.231, A.301, W.302, G.303, S.323, V.324, G.325, R.326 Chain B: W.358 Ligands: O8R.2, PEG.4 20 PLIP interactions: 18 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:M.24, A:R.326, B:W.358, B:W.358 Hydrogen bonds: A:P.23, A:C.25, A:A.57, A:Q.99, A:Q.99, A:H.181, A:R.231, A:R.231, A:W.302, A:G.303, A:G.325, A:R.326 Water bridges: A:F.304, A:G.305, A:A.327 Salt bridges: A:R.326 FMN.6: 19 residues within 4Å: Chain A: W.358 Chain B: P.22, P.23, M.24, C.25, A.57, Q.99, H.178, H.181, R.231, A.301, W.302, G.303, S.323, V.324, G.325, R.326 Ligands: MPD.5, O8R.7 20 PLIP interactions: 17 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:M.24, B:R.326, A:W.358, A:W.358 Hydrogen bonds: B:P.23, B:C.25, B:A.57, B:Q.99, B:Q.99, B:H.181, B:R.231, B:R.231, B:W.302, B:G.303, B:G.325, B:R.326 Water bridges: B:F.304, B:A.327, A:Y.362 Salt bridges: B:R.326

2 x O8R: 2-methoxyethyl (2~{Z})-2-hydroxyimino-3-oxidanylidene-butanoate(Non-covalent)

O8R.2: 8 residues within 4Å: Chain A: Y.27, I.66, H.178, H.181, Y.183, F.269, W.302 Ligands: FMN.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.178, A:H.181, A:Y.183 Water bridges: A:K.106 Salt bridges: A:H.181 O8R.7: 8 residues within 4Å: Chain B: Y.27, I.66, H.178, H.181, Y.183, F.269, W.302 Ligands: FMN.6 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.178, B:H.181, B:Y.183 Water bridges: B:K.106 Salt bridges: B:H.181

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 5 residues within 4Å: Chain A: R.47, A.91, A.92, P.352 Chain B: W.37 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:N.35, A:R.47, A:A.92 PEG.4: 5 residues within 4Å: Chain A: W.278, W.302, R.326 Chain B: W.358 Ligands: FMN.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.326 PEG.8: 1 residues within 4Å: Chain A: F.337 No protein-ligand interaction detected (PLIP) PEG.10: 7 residues within 4Å: Chain B: V.60, A.61, P.62, W.74, D.159, D.162, R.166 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.162, B:R.166, B:R.166

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.5: 5 residues within 4Å: Chain A: W.358, R.361 Chain B: W.302, R.326 Ligands: FMN.6 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.358, A:W.358, B:W.302 MPD.9: 6 residues within 4Å: Chain A: M.28, D.36, W.37 Chain B: R.47, A.91, A.92 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:D.36

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Breukelaar, W.B. et al., Mechanistic Insights into the Ene-Reductase-Catalyzed Promiscuous Reduction of Oximes to Amines. Acs Catalysis (2023)

Release Date

2023-03-01

Peptides

Xenobiotic reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Xenobiotic reductase

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