SMTL ID : 4gbu.1

OYE1-W116A in complex with aromatic product of S-carvone dismutation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.18 Å

Oligo State

homo-dimer

Ligands

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

MG.1: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.7: 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.23: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

0WV.2: 10 residues within 4Å: Chain A: T.38, G.73, Y.83, A.117, H.192, N.195, Y.197, F.251, Y.376 Ligands: FMN.12 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.38, A:Y.83, A:A.117, A:F.251 Hydrogen bonds: A:H.192, A:N.195 0WV.18: 10 residues within 4Å: Chain B: T.38, G.73, Y.83, A.117, H.192, N.195, Y.197, F.251, Y.376 Ligands: FMN.28 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:T.38, B:Y.83, B:A.117, B:F.251 Hydrogen bonds: B:H.192, B:N.195

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.13: 3 residues within 4Å: Chain A: V.4, K.5, K.369 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain B: Y.83, D.84, F.124, N.127 Ligand excluded by PLIP CL.29: 3 residues within 4Å: Chain B: V.4, K.5, K.369 Ligand excluded by PLIP

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

NA.4: 2 residues within 4Å: Chain A: Y.376 Ligands: 1PE.10 No protein-ligand interaction detected (PLIP) NA.8: 3 residues within 4Å: Chain A: Q.10, A.11 Ligands: 1PE.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.11 NA.9: 2 residues within 4Å: Chain A: W.53 Ligands: 1PE.5 No protein-ligand interaction detected (PLIP) NA.14: 2 residues within 4Å: Chain A: H.381 Ligands: 1PE.15 No protein-ligand interaction detected (PLIP) NA.16: 1 residues within 4Å: Ligands: 1PE.6 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.315 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 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.53 NA.30: 2 residues within 4Å: Chain B: H.381 Ligands: 1PE.31 No protein-ligand interaction detected (PLIP) NA.32: 1 residues within 4Å: Ligands: 1PE.22 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.311

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

1PE.5: 4 residues within 4Å: Chain A: D.52, W.53, A.380 Ligands: NA.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.380 Water bridges: A:D.52 1PE.6: 8 residues within 4Å: Chain A: D.311, Y.314, D.340 Chain B: E.306, G.307, G.308, S.309 Ligands: NA.16 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.323 Water bridges: A:D.311, A:E.337 1PE.10: 6 residues within 4Å: Chain A: M.40, Y.83, F.124, F.297, Y.376 Ligands: NA.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.376 1PE.11: 7 residues within 4Å: Chain A: P.9, Q.10, A.11, R.335, K.363, G.364 Ligands: NA.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.11, A:R.335 Water bridges: A:R.335 1PE.15: 7 residues within 4Å: Chain A: D.371, H.381, D.385, Y.386, 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 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.380 1PE.22: 8 residues within 4Å: Chain A: E.306, G.307, G.308, S.309 Chain B: D.311, Y.314, D.340 Ligands: NA.32 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.323 Water bridges: B:D.311 1PE.26: 6 residues within 4Å: Chain B: M.40, Y.83, F.124, F.297, Y.376 Ligands: NA.20 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.376 1PE.27: 7 residues within 4Å: Chain B: P.9, Q.10, A.11, R.335, K.363, G.364 Ligands: NA.24 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.11, B:R.335 Water bridges: B:R.335 1PE.31: 7 residues within 4Å: Chain B: D.371, H.381, D.385, Y.386, P.387, W.397 Ligands: NA.30 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.385

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:E.300, A:G.325, A:F.327, A:F.350 Salt bridges: A:R.349 FMN.28: 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.18 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

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

2012-08-29

Peptides

NADPH dehydrogenase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

NADPH dehydrogenase 1

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