SMTL ID : 3cav.2 (1 other biounit)

Crystal structure of 5beta-reductase (AKR1D1) in complex with NADP+ and 5beta-pregnan-3,20-dione

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

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

NAP.1: 28 residues within 4Å: Chain A: G.24, T.25, Y.26, D.53, Y.58, K.87, S.169, N.170, Q.193, Y.219, S.220, P.221, L.222, G.223, T.224, S.225, L.239, A.256, I.271, P.272, K.273, S.274, F.275, N.276, R.279, E.282, N.283 Ligands: CI2.2 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:T.25, A:Y.26, A:D.53, A:S.169, A:N.170, A:Q.193, A:S.220, A:L.222, A:T.224, A:K.273, A:S.274, A:F.275, A:E.282, A:N.283 Water bridges: A:Y.58, A:S.225, A:T.254 Salt bridges: A:K.273, A:R.279 pi-Stacking: A:Y.219 pi-Cation interactions: A:R.279, A:R.279

1 x CI2: (5BETA)-PREGNANE-3,20-DIONE(Non-covalent)

CI2.2: 6 residues within 4Å: Chain A: Y.26, Y.58, Y.132, W.230, W.314 Ligands: NAP.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.230, A:W.230, A:W.230, A:W.314 Hydrogen bonds: A:Y.58, A:Y.58

1 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.3: 4 residues within 4Å: Chain A: C.148, L.178, K.182, P.183 No protein-ligand interaction detected (PLIP)

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

EDO.4: 5 residues within 4Å: Chain A: A.6, S.7, H.8, R.9, R.50 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.8, A:R.9 Water bridges: A:A.6, A:S.7, A:R.9 EDO.5: 5 residues within 4Å: Chain A: E.152, E.155, A.156, D.159, K.186 3 PLIP interactions: 3 interactions with chain A Water bridges: A:G.184, A:G.184, A:K.186

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Faucher, F. et al., The crystal structure of human Delta4-3-ketosteroid 5beta-reductase defines the functional role of the residues of the catalytic tetrad in the steroid double bond reduction mechanism. Biochemistry (2008)

Release Date

2008-07-29

Peptides

3-oxo-5-beta-steroid 4-dehydrogenase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

3-oxo-5-beta-steroid 4-dehydrogenase

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