SMTL ID : 6yc8.1

Crystal structure of KRED1-Pglu enzyme

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

monomer

Ligands

1 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 31 residues within 4Å: Chain A: G.9, A.10, S.11, R.12, G.13, L.14, A.35, R.36, S.37, G.57, D.58, V.59, N.85, A.86, G.87, V.88, R.105, V.109, V.135, S.136, S.137, Y.150, K.154, P.178, G.179, V.180, V.181, T.183, M.185, Q.186 Ligands: ACT.2 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:P.178 Hydrogen bonds: A:S.11, A:S.11, A:R.12, A:R.12, A:L.14, A:R.36, A:S.37, A:D.58, A:V.59, A:N.85, A:G.87, A:R.105, A:Y.150, A:K.154, A:V.181, A:V.181, A:T.183, A:D.184, A:M.185 Water bridges: A:R.12, A:R.12, A:G.15, A:N.85 Salt bridges: A:R.12, A:R.12, A:R.36 pi-Cation interactions: A:R.36

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 6 residues within 4Å: Chain A: S.137, W.147, Y.150, M.185, Q.186 Ligands: NAP.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.147 Hydrogen bonds: A:S.137, A:Q.186 Water bridges: A:G.138

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.3: 4 residues within 4Å: Chain A: R.126, E.167, E.168, L.170 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.168 Water bridges: A:R.126, A:E.168 Salt bridges: A:E.168, A:E.168

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

PGE.4: 4 residues within 4Å: Chain A: F.76, G.77, R.78, Q.127 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.78, A:R.78 PGE.5: 2 residues within 4Å: Chain A: R.36, S.37 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.38

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

PEG.6: 5 residues within 4Å: Chain A: V.73, A.74, K.75, F.76, G.77 No protein-ligand interaction detected (PLIP) PEG.7: 2 residues within 4Å: Chain A: L.162, N.237 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.237 PEG.8: 4 residues within 4Å: Chain A: A.24, R.25, N.26, A.27 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.24, A:A.27 PEG.9: 5 residues within 4Å: Chain A: D.58, T.60, R.61, R.105, E.108 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.60, A:R.61, A:R.105

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.10: 4 residues within 4Å: Chain A: H.94, Q.195, N.196, M.197 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.94 EDO.11: 3 residues within 4Å: Chain A: P.123, Y.124, Q.127 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rabuffetti, M. et al., Structural insights into the desymmetrization of bulky 1,2-dicarbonyls through enzymatic monoreduction. Bioorg.Chem. (2021)

Release Date

2021-02-10

Peptides

Ketoreductase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ketoreductase