SMTL ID : 8au8.1

Xenobiotic reductase A from P. putida in complex with ethyl (Z)-2-(hydroxyimino)-3-oxopentanoate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

homo-dimer

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 17 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, V.324, G.325, R.326 Chain B: W.358 Ligands: O8I.2 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:M.24, A:R.326 Hydrogen bonds: A:P.23, A:C.25, A:A.57, A:Q.99, A:Q.99, 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.9: 17 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, V.324, G.325, R.326 Ligands: O8I.10 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:M.24, B:R.326 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:G.305, B:A.327 Salt bridges: B:R.326

3 x O8I: ethyl (2~{Z})-2-hydroxyimino-3-oxidanylidene-pentanoate(Non-covalent)

O8I.2: 11 residues within 4Å: Chain A: C.25, Y.27, A.57, I.66, H.178, H.181, Y.183, F.269, W.302 Ligands: FMN.1, PEG.6 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.57, A:I.66, A:Y.183, A:F.269 Hydrogen bonds: A:Y.27, A:Y.183 Salt bridges: A:H.181 O8I.4: 6 residues within 4Å: Chain A: I.135, A.136, F.137, H.192, I.271, E.273 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.135, A:E.273 Hydrogen bonds: A:H.192 O8I.10: 10 residues within 4Å: Chain B: C.25, Y.27, A.57, I.66, H.178, H.181, Y.183, F.269, W.302 Ligands: FMN.9 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.57, B:I.66, B:Y.183, B:F.269 Hydrogen bonds: B:H.181 Salt bridges: B:H.181

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

PEG.3: 4 residues within 4Å: Chain A: P.285, E.288, A.316, Q.318 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.317, A:Q.318 Water bridges: A:E.288, A:E.288 PEG.6: 5 residues within 4Å: Chain A: K.106, F.137, H.140, P.272 Ligands: O8I.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.106, A:H.140 Water bridges: A:H.140, A:H.140 PEG.12: 4 residues within 4Å: Chain B: K.106, F.137, H.140, P.272 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.106, B:K.106

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

CL.5: 4 residues within 4Å: Chain A: R.47, A.88 Chain B: D.36 Ligands: MPD.8 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain B: F.5, R.16, N.17 Ligand excluded by PLIP

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

MPD.7: 6 residues within 4Å: Chain A: M.28, D.36, W.37 Chain B: R.47, A.91, A.92 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:D.36, A:W.37 MPD.8: 7 residues within 4Å: Chain A: R.47, A.91, A.92 Chain B: M.28, D.36, W.37 Ligands: CL.5 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:D.36, B:W.37

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.13: 7 residues within 4Å: Chain B: G.120, A.121, D.123, G.126, W.127, N.143, V.144 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.123, B:D.123, B:G.126, B:V.144 Water bridges: B:T.129, B:N.143, B:N.143

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
A

B
B

Xenobiotic reductase

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