SMTL ID : 8g93.1

Crystal structures of 17-beta-hydroxysteroid dehydrogenase 13

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 28 residues within 4Å: Chain A: G.44, G.46, H.47, G.48, I.49, D.68, I.69, N.70, V.93, D.94, C.95, G.96, N.121, A.122, G.123, I.144, V.171, A.172, S.173, Y.186, K.190, P.219, V.220, F.221, V.222, T.224, F.226 Ligands: YXW.2 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:P.219 Hydrogen bonds: A:G.44, A:G.46, A:I.49, A:I.69, A:D.94, A:C.95, A:G.96, A:N.121, A:G.123, A:Y.186, A:K.190, A:V.222, A:V.222, A:T.224, A:T.224 Water bridges: A:H.47, A:G.50, A:G.50 Salt bridges: A:H.47 NAD.3: 26 residues within 4Å: Chain B: G.44, G.46, H.47, G.48, I.49, D.68, I.69, V.93, D.94, C.95, N.121, A.122, G.123, I.144, V.171, A.172, S.173, Y.186, K.190, P.219, V.220, F.221, V.222, T.224, F.226 Ligands: YXW.4 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:P.219 Hydrogen bonds: B:G.44, B:G.46, B:I.49, B:I.69, B:D.94, B:D.94, B:C.95, B:G.96, B:N.121, B:K.190, B:V.222, B:V.222, B:T.224 Water bridges: B:G.50, B:N.121 Salt bridges: B:H.47

2 x YXW: 3-fluoro-N-({(1r,4r)-4-[(2-fluorophenoxy)methyl]-1-hydroxycyclohexyl}methyl)-4-hydroxybenzamide(Non-covalent)

YXW.2: 18 residues within 4Å: Chain A: P.127, S.173, V.174, C.175, I.180, P.181, Y.182, L.183, Y.186, P.219, V.220, F.221, F.226, T.227, K.228, P.230 Chain B: A.206 Ligands: NAD.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.181, A:L.183, A:Y.186, A:F.221 Hydrogen bonds: A:S.173, A:T.227 Halogen bonds: A:P.219 YXW.4: 19 residues within 4Å: Chain A: A.206 Chain B: P.127, S.173, V.174, C.175, I.180, P.181, Y.182, L.183, Y.186, P.219, V.220, F.221, F.226, T.227, K.228, N.229, P.230 Ligands: NAD.3 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.181, B:L.183, B:L.183, B:Y.186, B:F.221, B:T.227, A:A.206 Hydrogen bonds: B:S.173, B:Y.186, B:T.227, B:T.227, B:K.228, B:K.228 Halogen bonds: B:P.219

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, S. et al., Structural basis of lipid-droplet localization of 17-beta-hydroxysteroid dehydrogenase 13. Nat Commun (2023)

Release Date

2023-08-09

Peptides

Hydroxysteroid 17-beta dehydrogenase 13: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Hydroxysteroid 17-beta dehydrogenase 13