SMTL ID : 3upw.1

Pichia Stipitis OYE2.6 complexed with nicotinamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-dimer

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 23 residues within 4Å: Chain A: P.32, P.33, T.34, T.35, R.36, A.68, Q.111, H.188, H.191, R.240, V.286, V.290, G.292, N.293, A.319, G.320, N.321, F.345, S.346, R.347, F.373, Y.374 Ligands: NCA.5 25 PLIP interactions: 25 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: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: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 Salt bridges: A:R.347 FMN.10: 23 residues within 4Å: Chain B: P.32, P.33, T.34, T.35, R.36, A.68, Q.111, H.188, H.191, R.240, V.286, V.290, G.292, N.293, A.319, G.320, N.321, F.345, S.346, R.347, F.373, Y.374 Ligands: NCA.14 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: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: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

6 x MLA: MALONIC ACID(Non-covalent)

MLA.2: 5 residues within 4Å: Chain A: F.37, Y.78, E.79, G.80 Ligands: NA.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.78 Hydrogen bonds: A:E.79, A:E.79, A:E.79, A:G.80 Water bridges: A:D.120 MLA.3: 7 residues within 4Å: Chain A: E.41, H.43, S.76, Y.78, V.123, T.126, R.127 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.123 Hydrogen bonds: A:S.76 Water bridges: A:R.127 Salt bridges: A:H.43, A:H.43, A:R.127, A:R.127 MLA.4: 5 residues within 4Å: Chain A: K.10, R.360 Chain B: T.58, N.354, W.357 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Water bridges: A:R.360, A:R.360 Salt bridges: A:K.10, A:K.10, A:R.360, A:R.360 Hydrophobic interactions: B:N.354 Hydrogen bonds: B:N.354, B:W.357 MLA.11: 5 residues within 4Å: Chain B: F.37, Y.78, E.79, G.80 Ligands: NA.15 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.78 Hydrogen bonds: B:E.79, B:E.79, B:G.80 MLA.12: 7 residues within 4Å: Chain B: E.41, H.43, S.76, Y.78, V.123, T.126, R.127 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:V.123 Hydrogen bonds: B:S.76 Water bridges: B:R.127 Salt bridges: B:H.43, B:H.43, B:R.127, B:R.127 MLA.13: 5 residues within 4Å: Chain A: T.58, N.354, W.357 Chain B: K.10, R.360 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Water bridges: B:R.360, B:R.360 Salt bridges: B:K.10, B:K.10, B:R.360, B:R.360 Hydrophobic interactions: A:N.354 Hydrogen bonds: A:T.58, A:N.354, A:W.357

2 x NCA: NICOTINAMIDE(Non-covalent)

NCA.5: 11 residues within 4Å: Chain A: T.35, A.68, I.113, H.188, H.191, Y.193, F.247, G.292, N.293, Y.374 Ligands: FMN.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.188 Water bridges: A:Y.78 NCA.14: 11 residues within 4Å: Chain B: T.35, A.68, I.113, H.188, H.191, Y.193, F.247, G.292, N.293, Y.374 Ligands: FMN.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.188, B:H.191

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

NA.6: 1 residues within 4Å: Ligands: MLA.2 3 PLIP interactions: 3 interactions with chain A Water bridges: A:V.118, A:V.118, A:V.118 NA.7: 5 residues within 4Å: Chain A: H.191, D.196, Q.200, S.242, A.245 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.191, A:G.192, A:D.196, A:Q.200 Water bridges: A:S.242 NA.8: 2 residues within 4Å: Chain A: N.104 Chain B: Q.26 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.26 Water bridges: B:S.17 NA.9: 3 residues within 4Å: Chain A: D.335, D.338, T.341 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.338 NA.15: 1 residues within 4Å: Ligands: MLA.11 3 PLIP interactions: 3 interactions with chain B Water bridges: B:V.118, B:V.118, B:V.118 NA.16: 5 residues within 4Å: Chain B: H.191, D.196, Q.200, S.242, A.245 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.191, B:G.192, B:D.196, B:Q.200 Water bridges: B:S.242 NA.17: 2 residues within 4Å: Chain A: Q.26 Chain B: N.104 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.26 Water bridges: A:S.17 NA.18: 3 residues within 4Å: Chain B: D.335, D.338, T.341 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.335, B:T.341

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

Old Yellow Enzyme 2.6 (OYE2.6), NADPH dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Old Yellow Enzyme 2.6 (OYE2.6), NADPH dehydrogenase

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