SMTL ID : 4k8e.1

OYE1-W116V complexed with the aromatic product of (R)-carvone dismutation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.27 Å

Oligo State

homo-dimer

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 27 residues within 4Å: Chain A: P.35, P.36, L.37, T.38, R.39, E.72, G.73, Q.115, H.192, N.195, R.244, V.289, V.293, P.296, F.297, A.324, G.325, N.326, F.327, Y.347, G.348, R.349, I.352, F.375, Y.376 Ligands: 0WV.4, CL.6 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:L.37, A:P.296, A:F.297, A:F.297, A:R.349, A:F.375, A:Y.376 Hydrogen bonds: A:T.38, A:T.38, A:G.73, A:Q.115, A:Q.115, A:H.192, A:N.195, A:R.244, A:R.244, A:N.326, A:G.348, A:R.349, A:R.349 Water bridges: A:E.300, A:E.300, A:G.325, A:F.327, A:F.350 Salt bridges: A:R.349 FMN.16: 27 residues within 4Å: Chain B: P.35, P.36, L.37, T.38, R.39, E.72, G.73, Q.115, H.192, N.195, R.244, V.289, V.293, P.296, F.297, A.324, G.325, N.326, F.327, Y.347, G.348, R.349, I.352, F.375, Y.376 Ligands: 0WV.19, CL.21 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:L.37, B:P.296, B:F.297, B:F.297, B:R.349, B:F.375, B:Y.376 Hydrogen bonds: B:T.38, B:T.38, B:G.73, B:Q.115, B:Q.115, B:H.192, B:N.195, B:R.244, B:R.244, B:N.326, B:G.348, B:R.349, B:R.349 Water bridges: B:G.325, B:F.327, B:R.349, B:R.349, B:F.350 Salt bridges: B:R.349

4 x MG: MAGNESIUM ION(Non-functional Binders)

MG.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.20: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

CL.3: 4 residues within 4Å: Chain A: Y.83, D.84, F.124, N.127 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain A: H.192, N.195, Y.197 Ligands: FMN.1, 0WV.4 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain B: Y.83, D.84, F.124, N.127 Ligand excluded by PLIP CL.21: 5 residues within 4Å: Chain B: H.192, N.195, Y.197 Ligands: FMN.16, 0WV.19 Ligand excluded by PLIP

2 x 0WV: 2-methyl-5-(prop-1-en-2-yl)phenol(Non-covalent)

0WV.4: 18 residues within 4Å: Chain A: T.38, M.40, G.73, F.75, Y.83, A.86, Q.115, V.117, L.119, H.192, N.195, Y.197, F.251, P.296, F.297, Y.376 Ligands: FMN.1, CL.6 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:T.38, A:Y.83, A:F.251, A:P.296 Hydrogen bonds: A:H.192, A:N.195, A:Y.197 0WV.19: 18 residues within 4Å: Chain B: T.38, M.40, G.73, F.75, Y.83, A.86, Q.115, V.117, L.119, H.192, N.195, Y.197, F.251, P.296, F.297, Y.376 Ligands: FMN.16, CL.21 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:T.38, B:Y.83, B:F.251, B:P.296 Hydrogen bonds: B:H.192, B:N.195, B:Y.197

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

PEG.7: 6 residues within 4Å: Chain A: D.371, H.381, G.382, D.385, Y.386, P.387 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.385 Water bridges: A:D.371 PEG.22: 6 residues within 4Å: Chain B: D.371, H.381, G.382, D.385, Y.386, P.387 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.385 Water bridges: B:S.2, B:D.371, B:D.371, B:D.385

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

NA.8: 3 residues within 4Å: Chain A: D.52, W.53 Ligands: PGE.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.53 NA.10: 3 residues within 4Å: Chain A: Q.10, A.11 Ligands: PGE.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.11 NA.11: 2 residues within 4Å: Chain A: Y.376 Ligands: PGE.12 No protein-ligand interaction detected (PLIP) NA.13: 3 residues within 4Å: Chain B: Y.314, S.315 Ligands: PGE.14 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.311, B:S.315 NA.23: 3 residues within 4Å: Chain B: D.52, W.53 Ligands: PGE.30 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.53 NA.25: 3 residues within 4Å: Chain B: Q.10, A.11 Ligands: PGE.24 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.11 NA.26: 2 residues within 4Å: Chain B: Y.376 Ligands: PGE.27 No protein-ligand interaction detected (PLIP) NA.28: 3 residues within 4Å: Chain A: Y.314, S.315 Ligands: PGE.29 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.311, A:S.315

8 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.9: 7 residues within 4Å: Chain A: Q.10, A.11, D.14, R.335, K.363, G.364 Ligands: NA.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.11, A:A.11, A:R.335, A:G.364 PGE.12: 7 residues within 4Å: Chain A: M.40, Y.83, F.124, F.251, F.297, Y.376 Ligands: NA.11 No protein-ligand interaction detected (PLIP) PGE.14: 11 residues within 4Å: Chain A: E.306, G.307, G.308, S.309 Chain B: D.311, Y.314, S.315, R.323, D.340, R.342 Ligands: NA.13 No protein-ligand interaction detected (PLIP) PGE.15: 4 residues within 4Å: Chain A: D.52, W.53, A.380 Ligands: NA.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.53 Water bridges: A:D.52 PGE.24: 7 residues within 4Å: Chain B: Q.10, A.11, D.14, R.335, K.363, G.364 Ligands: NA.25 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.11, B:A.11, B:R.335, B:G.364 PGE.27: 7 residues within 4Å: Chain B: M.40, Y.83, F.124, F.251, F.297, Y.376 Ligands: NA.26 No protein-ligand interaction detected (PLIP) PGE.29: 11 residues within 4Å: Chain A: D.311, Y.314, S.315, R.323, D.340, R.342 Chain B: E.306, G.307, G.308, S.309 Ligands: NA.28 No protein-ligand interaction detected (PLIP) PGE.30: 4 residues within 4Å: Chain B: D.52, W.53, A.380 Ligands: NA.23 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.53

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pompeu, Y.A. et al., X‑ray Crystallography Reveals How Subtle Changes Control the Orientation of Substrate Binding in an Alkene Reductase. ACS CATALYSIS (2013)

Release Date

2013-10-09

Peptides

NADPH dehydrogenase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

NADPH dehydrogenase 1

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