SMTL ID : 3tjl.1

Crystal Structure of a Novel OYE from the Xylose-fermenting Fungus P. stipitis

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: 20 residues within 4Å: Chain A: P.32, P.33, T.34, T.35, A.68, Q.111, H.188, H.191, R.240, V.290, G.292, N.293, G.320, N.321, F.345, S.346, R.347, F.373, Y.374 Ligands: MLA.8 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:T.34, A:N.293, A:R.347, A:F.373, A:F.373, A:Y.374 Hydrogen bonds: A:P.33, A:T.35, A:A.68, A:Q.111, A:Q.111, A:R.240, A:R.240, A:N.321, A:G.344, A:S.346, A:S.346, A:R.347 Water bridges: A:T.35, A:G.320, A:G.320, A:R.347, A:R.347, A:Y.348, A:Y.374 Salt bridges: A:R.347 FMN.9: 20 residues within 4Å: Chain B: P.32, P.33, T.34, T.35, A.68, Q.111, H.188, H.191, R.240, V.290, G.292, N.293, G.320, N.321, F.345, S.346, R.347, F.373, Y.374 Ligands: MLA.16 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:T.34, B:N.293, B:R.347, B:F.373, B:F.373, B:Y.374 Hydrogen bonds: B:P.33, B:T.35, B:T.35, B:A.68, B:Q.111, B:Q.111, B:H.191, B:R.240, B:R.240, B:N.321, B:G.344, B:S.346, B:S.346, B:R.347 Water bridges: B:G.320, B:G.320, B:R.347, B:R.347, B:Y.348 Salt bridges: B:R.347

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

NA.2: 1 residues within 4Å: Chain A: Q.26 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.26 NA.3: 3 residues within 4Å: Chain A: D.335, D.338, T.341 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.309, A:S.309 NA.4: 2 residues within 4Å: Chain A: E.139 Ligands: NA.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.139 NA.5: 2 residues within 4Å: Ligands: NA.4, MLA.6 5 PLIP interactions: 5 interactions with chain A Water bridges: A:V.118, A:V.118, A:E.139, A:E.139, A:E.139 NA.10: 1 residues within 4Å: Chain B: Q.26 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.26 NA.11: 3 residues within 4Å: Chain B: D.335, D.338, T.341 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.309, B:S.309, B:T.341 NA.12: 2 residues within 4Å: Chain B: E.139 Ligands: NA.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.139 NA.13: 2 residues within 4Å: Ligands: NA.12, MLA.14 3 PLIP interactions: 3 interactions with chain B Water bridges: B:V.118, B:V.118, B:E.139

6 x MLA: MALONIC ACID(Non-covalent)

MLA.6: 5 residues within 4Å: Chain A: F.37, Y.78, E.79, G.80 Ligands: NA.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.79, A:G.80 Water bridges: A:G.77 MLA.7: 6 residues within 4Å: Chain A: E.41, H.43, S.76, Y.78, V.123, R.127 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.123 Hydrogen bonds: A:S.76, A:S.76 Water bridges: A:G.77, A:R.127 Salt bridges: A:H.43, A:H.43, A:R.127, A:R.127 MLA.8: 8 residues within 4Å: Chain A: I.113, H.188, H.191, Y.193, F.247, G.292, N.293 Ligands: FMN.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.193 Water bridges: A:T.35, A:T.35, A:Y.374, A:Y.374 Salt bridges: A:H.188, A:H.191, A:H.191 MLA.14: 5 residues within 4Å: Chain B: F.37, Y.78, E.79, G.80 Ligands: NA.13 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.79, B:G.80 Water bridges: B:G.77 MLA.15: 6 residues within 4Å: Chain B: E.41, H.43, S.76, Y.78, V.123, R.127 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.123 Hydrogen bonds: B:S.76, B:S.76 Water bridges: B:G.77, B:R.127 Salt bridges: B:H.43, B:H.43, B:R.127, B:R.127 MLA.16: 8 residues within 4Å: Chain B: I.113, H.188, H.191, Y.193, F.247, G.292, N.293 Ligands: FMN.9 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.193 Hydrogen bonds: B:Y.193 Water bridges: B:T.35, B:Y.193, B:Y.374 Salt bridges: B:H.188, B:H.191, B:H.191

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pompeu, Y.A. et al., Structural and Catalytic Characterization of Pichia stipitis OYE 2.6, a Useful Biocatalyst for Asymmetric Alkene Reductions. Adv.Synth.Catal. (2012)

Release Date

2012-07-11

Peptides

NADPH dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

NADPH dehydrogenase

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