SMTL ID : 4e13.1

Substrate-directed dual catalysis of dicarbonyl compounds by diketoreductase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.08 Å

Oligo State

homo-dimer

Ligands

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 22 residues within 4Å: Chain A: G.11, T.12, G.13, V.14, L.15, Y.33, D.34, I.35, A.92, V.93, P.94, E.95, L.99, K.100, I.103, N.120, S.121, S.122, H.143, F.144, N.146 Ligands: 1PE.6 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.15, A:L.15 Hydrogen bonds: A:T.12, A:T.12, A:V.14, A:L.15, A:D.34, A:E.95, A:K.100, A:K.100, A:N.120, A:S.122 Water bridges: A:G.13, A:G.13, A:N.146 NAD.8: 22 residues within 4Å: Chain B: G.11, T.12, G.13, V.14, L.15, Y.33, D.34, I.35, A.92, V.93, P.94, E.95, L.99, K.100, I.103, N.120, S.121, S.122, H.143, F.144, N.146 Ligands: 1PE.13 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:L.15, B:L.15 Hydrogen bonds: B:T.12, B:T.12, B:V.14, B:L.15, B:E.95, B:K.100, B:K.100, B:N.120, B:S.122 Water bridges: B:G.13, B:G.13, B:N.146

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 2 residues within 4Å: Chain A: P.253, R.256 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.253 GOL.3: 4 residues within 4Å: Chain A: I.235, I.238, V.239 Chain B: G.225 No protein-ligand interaction detected (PLIP) GOL.4: 4 residues within 4Å: Chain A: E.234, Y.281, R.282, Y.283 No protein-ligand interaction detected (PLIP) GOL.5: 7 residues within 4Å: Chain A: R.74, Q.81, A.82, V.83, K.84, D.85, A.86 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.74, A:Q.81, A:V.83, A:D.85 Water bridges: A:T.8 GOL.9: 2 residues within 4Å: Chain B: P.253, R.256 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.253 GOL.10: 4 residues within 4Å: Chain A: G.225 Chain B: I.235, I.238, V.239 No protein-ligand interaction detected (PLIP) GOL.11: 4 residues within 4Å: Chain B: E.234, Y.281, R.282, Y.283 No protein-ligand interaction detected (PLIP) GOL.12: 7 residues within 4Å: Chain B: R.74, Q.81, A.82, V.83, K.84, D.85, A.86 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.74, B:Q.81, B:V.83, B:D.85

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

1PE.6: 9 residues within 4Å: Chain A: S.122, N.194, V.198, L.201, D.202, V.239, I.247, S.248 Ligands: NAD.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.122, A:S.248 1PE.13: 9 residues within 4Å: Chain B: S.122, N.194, V.198, L.201, D.202, V.239, I.247, S.248 Ligands: NAD.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.122, B:S.248

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 6 residues within 4Å: Chain A: V.239, G.240, L.241, T.242, T.243, L.272 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.239, A:T.242, A:T.242, A:T.243 Water bridges: A:A.275 SO4.14: 6 residues within 4Å: Chain B: V.239, G.240, L.241, T.242, T.243, L.272 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:V.239, B:T.242, B:T.242, B:T.243, B:T.243 Water bridges: B:A.275

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lu, M. et al., Dual catalysis mode for the dicarbonyl reduction catalyzed by diketoreductase. Chem.Commun.(Camb.) (2012)

Release Date

2012-11-14

Peptides

Diketoreductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Diketoreductase

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