SMTL ID : 4k7y.1

Oye1-w116t

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

homo-dimer

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 26 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: CL.7 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:G.325, A:F.350 Salt bridges: A:R.349 FMN.11: 26 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: CL.17 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:G.325, B:R.349, B:R.349, B:F.350 Salt bridges: B:R.349

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

MG.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.6: 4 residues within 4Å: Chain A: D.373, T.374, Y.376, Q.377 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.373, A:Y.376, H2O.21 MG.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.16: 4 residues within 4Å: Chain B: D.373, T.374, Y.376, Q.377 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.373, B:Y.376, H2O.47 MG.19: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

PEG.3: 8 residues within 4Å: Chain A: D.371, T.374, H.381, G.382, D.385, Y.386, P.387, W.397 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.385 PEG.4: 4 residues within 4Å: Chain A: H.44, D.84, N.85, R.130 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.85 PEG.5: 3 residues within 4Å: Chain A: W.53, A.380 Ligands: NA.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.53 PEG.13: 8 residues within 4Å: Chain B: D.371, T.374, H.381, G.382, D.385, Y.386, P.387, W.397 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.385 Water bridges: B:D.371 PEG.14: 4 residues within 4Å: Chain B: H.44, D.84, N.85, R.130 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.84, B:N.85 PEG.15: 3 residues within 4Å: Chain B: W.53, A.380 Ligands: NA.20 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.53

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

CL.7: 4 residues within 4Å: Chain A: H.192, N.195, Y.197 Ligands: FMN.1 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: Y.83, D.84, F.124, N.127 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain B: H.192, N.195, Y.197 Ligands: FMN.11 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain B: Y.83, D.84, F.124, N.127 Ligand excluded by PLIP

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

NA.10: 3 residues within 4Å: Chain A: D.52, W.53 Ligands: PEG.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.53 NA.20: 3 residues within 4Å: Chain B: D.52, W.53 Ligands: PEG.15 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