SMTL ID : 4h4i.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

homo-dimer

Ligands

6 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.1: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.11: 1 residues within 4Å: Chain A: E.337 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.337, H2O.20, H2O.21, H2O.22, H2O.23 MG.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.23: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.28: 1 residues within 4Å: Chain B: E.337 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.337, H2O.46, H2O.46, H2O.47, H2O.49

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

0WV.2: 9 residues within 4Å: Chain A: T.38, Y.83, H.192, N.195, Y.197, F.251, P.296, Y.376 Ligands: FMN.12 6 PLIP interactions: 6 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 0WV.19: 9 residues within 4Å: Chain B: T.38, Y.83, H.192, N.195, Y.197, F.251, P.296, Y.376 Ligands: FMN.29 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

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

NA.3: 2 residues within 4Å: Chain A: Y.376 Ligands: 1PE.9 No protein-ligand interaction detected (PLIP) NA.7: 3 residues within 4Å: Chain A: Q.10, A.11 Ligands: 1PE.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.11 NA.8: 2 residues within 4Å: Chain A: W.53 Ligands: 1PE.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.53 NA.14: 2 residues within 4Å: Chain A: H.381 Ligands: 1PE.15 No protein-ligand interaction detected (PLIP) NA.17: 1 residues within 4Å: Ligands: 1PE.5 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:D.311, B:S.309 NA.20: 2 residues within 4Å: Chain B: Y.376 Ligands: 1PE.26 No protein-ligand interaction detected (PLIP) NA.24: 3 residues within 4Å: Chain B: Q.10, A.11 Ligands: 1PE.27 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.11 NA.25: 2 residues within 4Å: Chain B: W.53 Ligands: 1PE.21 No protein-ligand interaction detected (PLIP) NA.31: 2 residues within 4Å: Chain B: H.381 Ligands: 1PE.32 No protein-ligand interaction detected (PLIP) NA.34: 1 residues within 4Å: Ligands: 1PE.22 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:S.309, B:D.311, B:S.315

10 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.4: 4 residues within 4Å: Chain A: D.52, W.53, A.380 Ligands: NA.8 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.52 1PE.5: 9 residues within 4Å: Chain A: D.311, Y.314, R.323, D.340 Chain B: E.306, G.307, G.308, S.309 Ligands: NA.17 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.323 Water bridges: A:D.311, A:Y.314, A:E.337, A:E.337 1PE.9: 6 residues within 4Å: Chain A: M.40, Y.83, F.124, F.297, Y.376 Ligands: NA.3 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.376, A:Y.376 1PE.10: 7 residues within 4Å: Chain A: P.9, Q.10, A.11, R.335, K.363, G.364 Ligands: NA.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.335 1PE.15: 6 residues within 4Å: Chain A: D.371, H.381, D.385, P.387, W.397 Ligands: NA.14 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.385 1PE.21: 4 residues within 4Å: Chain B: D.52, W.53, A.380 Ligands: NA.25 No protein-ligand interaction detected (PLIP) 1PE.22: 9 residues within 4Å: Chain A: E.306, G.307, G.308, S.309 Chain B: D.311, Y.314, R.323, D.340 Ligands: NA.34 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.323 Water bridges: B:D.311, B:Y.314, B:E.337, B:E.337 1PE.26: 6 residues within 4Å: Chain B: M.40, Y.83, F.124, F.297, Y.376 Ligands: NA.20 No protein-ligand interaction detected (PLIP) 1PE.27: 7 residues within 4Å: Chain B: P.9, Q.10, A.11, R.335, K.363, G.364 Ligands: NA.24 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.335 1PE.32: 6 residues within 4Å: Chain B: D.371, H.381, D.385, P.387, W.397 Ligands: NA.31 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.385 Water bridges: B:D.371

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.12: 19 residues within 4Å: Chain A: P.35, P.36, L.37, T.38, G.73, Q.115, H.192, N.195, R.244, P.296, F.297, G.325, N.326, Y.347, G.348, R.349, F.375, Y.376 Ligands: 0WV.2 24 PLIP interactions: 24 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:P.36, A:T.38, A:G.73, A:Q.115, A:Q.115, A:N.195, A:R.244, A:R.244, A:N.326, A:G.348, A:R.349 Water bridges: A:E.300, A:G.325, A:F.327, A:R.349, A:F.350 Salt bridges: A:R.349 FMN.29: 19 residues within 4Å: Chain B: P.35, P.36, L.37, T.38, G.73, Q.115, H.192, N.195, R.244, P.296, F.297, G.325, N.326, Y.347, G.348, R.349, F.375, Y.376 Ligands: 0WV.19 25 PLIP interactions: 25 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:P.36, B:T.38, B:T.38, B:G.73, B:Q.115, B:Q.115, B:N.195, B:R.244, B:R.244, B:N.326, B:G.348, 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 CL: CHLORIDE ION(Non-functional Binders)

CL.13: 3 residues within 4Å: Chain A: V.4, K.5, K.369 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain A: Y.83, D.84, F.124, N.127 Ligand excluded by PLIP CL.30: 3 residues within 4Å: Chain B: V.4, K.5, K.369 Ligand excluded by PLIP CL.33: 4 residues within 4Å: Chain B: Y.83, D.84, F.124, N.127 Ligand excluded by PLIP

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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