SMTL ID : 5cpl.1

The crystal structure of Xenobiotic reductase A (XenA) from Pseudomonas putida in complex with a nicotinamide mimic (mNH2)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

homo-dimer

Ligands

2 x 536: 1-benzyl-1,4,5,6-tetrahydropyridine-3-carboxamide(Non-covalent)

536.1: 13 residues within 4Å: Chain A: C.25, Y.27, A.57, I.66, H.178, H.181, Y.183, F.269, W.278, W.302, R.326 Chain B: W.358 Ligands: FNR.2 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:W.302, B:W.358, B:W.358 Hydrogen bonds: A:H.178, A:H.181, A:Y.183 536.3: 13 residues within 4Å: Chain A: W.358 Chain B: C.25, Y.27, A.57, I.66, H.178, H.181, Y.183, F.269, W.278, W.302, R.326 Ligands: FNR.5 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:W.302, A:W.358, A:W.358 Hydrogen bonds: B:H.178, B:H.181

2 x FNR: 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL(Non-covalent)

FNR.2: 21 residues within 4Å: Chain A: P.22, P.23, M.24, C.25, Q.26, Y.27, E.56, A.57, Q.99, H.178, H.181, R.231, A.301, W.302, G.303, V.324, G.325, R.326, L.329 Chain B: W.358 Ligands: 536.1 24 PLIP interactions: 22 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:M.24, A:R.326, A:L.329, B:W.358, B:W.358 Hydrogen bonds: A:C.25, A:A.57, A:Q.99, A:Q.99, A:H.178, A:H.181, A:R.231, A:R.231, A:W.302, A:G.303, A:G.325, A:R.326, A:R.326 Water bridges: A:F.304, A:G.305, A:R.326, A:R.326, A:A.327 Salt bridges: A:R.326 FNR.5: 21 residues within 4Å: Chain A: W.358 Chain B: P.22, P.23, M.24, C.25, Q.26, Y.27, E.56, A.57, Q.99, H.178, H.181, R.231, A.301, W.302, G.303, V.324, G.325, R.326, L.329 Ligands: 536.3 25 PLIP interactions: 23 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:M.24, B:R.326, B:L.329, A:W.358, A:W.358 Hydrogen bonds: B:C.25, B:A.57, B:Q.99, B:Q.99, B:H.178, B:H.181, B:R.231, B:R.231, B:W.302, B:G.303, B:G.325, B:R.326, B:R.326 Water bridges: B:F.304, B:G.305, B:G.305, B:S.323, B:R.326, B:R.326 Salt bridges: B:R.326

1 x CA: CALCIUM ION(Non-covalent)

CA.4: 4 residues within 4Å: Chain B: E.128, N.143, V.144, P.145 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.128, B:V.144, H2O.16, H2O.16, H2O.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Knaus, T. et al., Better than Nature: Nicotinamide Biomimetics That Outperform Natural Coenzymes. J.Am.Chem.Soc. (2016)

Release Date

2016-01-20

Peptides

Xenobiotic reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Xenobiotic reductase

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