SMTL ID : 8g9v.2 (3 other biounits)

Crystal structures of 17-beta-hydroxysteroid dehydrogenase 13

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.64 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, S.96, N.121, A.122, G.123, V.144, V.171, A.172, S.173, Y.186, K.190, P.219, V.220, F.221, V.222, T.224, F.226 Ligands: YYC.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:P.219 Hydrogen bonds: A:G.46, A:I.49, A:I.69, A:D.94, A:C.95, A:S.96, A:N.121, A:K.190, A:V.222, A:V.222, A:T.224 Water bridges: A:N.121, A:N.121 Salt bridges: A:H.47 NAD.8: 28 residues within 4Å: Chain B: G.44, G.46, H.47, G.48, I.49, D.68, I.69, N.70, V.93, D.94, C.95, S.96, N.121, A.122, G.123, V.144, V.171, A.172, S.173, Y.186, K.190, P.219, V.220, F.221, V.222, T.224, F.226 Ligands: YYC.9 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:C.95, B:S.96, B:N.121, B:K.190, B:V.222, B:V.222, B:T.224, B:T.224 Water bridges: B:G.50, B:N.121 Salt bridges: B:H.47

2 x YYC: 4-{[2,5-dimethyl-3-(4-methylbenzene-1-sulfonyl)benzene-1-sulfonyl]amino}benzoic acid(Non-covalent)

YYC.2: 17 residues within 4Å: Chain A: S.173, V.174, C.175, E.178, I.180, Y.186, P.219, V.220, F.221, F.226, T.227, P.230, P.236, I.264, F.267 Chain B: I.5 Ligands: NAD.1 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.174, A:V.174, A:I.180, A:V.220, A:F.221, A:F.221, A:P.230, B:I.5 Hydrogen bonds: A:S.173, A:Y.186, A:Y.186, A:F.221 YYC.9: 18 residues within 4Å: Chain B: S.173, V.174, C.175, E.178, I.180, Y.186, P.219, V.220, F.221, F.226, T.227, I.264, F.267, L.268, L.274, L.282 Ligands: NAD.8, CE1.10 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:V.174, B:V.174, B:I.180, B:V.220, B:F.221, B:F.221, B:F.267, B:F.267 Hydrogen bonds: B:S.173, B:S.173, B:Y.186, B:F.221, B:T.227

2 x CE1: O-DODECANYL OCTAETHYLENE GLYCOL(Non-covalent)

CE1.3: 4 residues within 4Å: Chain A: Y.17, E.21, V.24 Chain B: F.273 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.273, A:Y.17, A:E.21, A:V.24 CE1.10: 17 residues within 4Å: Chain B: E.178, I.180, L.183, F.221, T.227, K.228, F.267, L.270, Q.271, F.273, L.274, P.275, L.282, M.285, Q.286, Q.289 Ligands: YYC.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.286, B:Q.289

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

SO4.4: 3 residues within 4Å: Chain A: R.32, R.60, L.252 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.60 Salt bridges: A:R.32, A:R.60 SO4.5: 3 residues within 4Å: Chain A: N.265, R.269 Chain B: K.272 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.265 Salt bridges: A:R.269, B:K.272 SO4.6: 3 residues within 4Å: Chain A: K.255, K.256, M.257 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.256, A:M.257 Salt bridges: A:K.255, A:K.256 SO4.7: 2 residues within 4Å: Chain A: R.163, H.165 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.163, A:H.165

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

17-beta-hydroxysteroid dehydrogenase 13: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

17-beta-hydroxysteroid dehydrogenase 13

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