SMTL ID : 8g9v.1 (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 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:P.219 Hydrogen bonds: A:G.46, A:I.49, A:I.69, A:D.94, A:D.94, A:C.95, A:S.96, A:N.121, A:Y.186, A:K.190, A:V.222, A:V.222, A:T.224, A:T.224 Water bridges: A:G.50, A:N.121, A:T.124 Salt bridges: A:H.47 NAD.6: 29 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, T.227 Ligands: YYC.7 16 PLIP interactions: 16 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:S.96, B:N.121, B:K.190, B:V.222, B:V.222, B:T.224 Water bridges: B:G.50 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: 19 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, W.235, I.264, F.267, L.268, L.274, L.282 Ligands: NAD.1, CE1.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.174, A:V.174, A:I.180, A:V.220, A:F.221, A:W.235, A:F.267, A:F.267 Hydrogen bonds: A:S.173, A:S.173, A:F.221 pi-Stacking: A:W.235 YYC.7: 20 residues within 4Å: Chain A: I.5 Chain B: S.173, V.174, C.175, E.178, I.180, Y.186, P.219, V.220, F.221, F.226, T.227, P.230, S.231, T.232, I.264, F.267, L.268, N.283 Ligands: NAD.6 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.174, B:V.174, B:I.180, B:V.220, A:I.5 Hydrogen bonds: B:S.173, B:S.173, B:Y.186, B:F.221, B:T.227, B:S.231, B:T.232

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

CE1.3: 18 residues within 4Å: Chain A: E.178, I.180, F.221, T.227, K.228, P.230, W.235, F.267, L.270, Q.271, F.273, L.274, P.275, L.282, M.285, Q.286, Q.289 Ligands: YYC.2 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.273 Hydrogen bonds: A:Q.289

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

SO4.4: 5 residues within 4Å: Chain A: K.255, K.256, M.257 Chain B: P.275, E.276 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.256, A:M.257, B:E.276 Salt bridges: A:K.255 SO4.5: 3 residues within 4Å: Chain A: R.32, R.60, L.252 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.32, A:R.60 SO4.8: 3 residues within 4Å: Chain B: R.32, R.60, L.252 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.32, B:R.60 SO4.9: 4 residues within 4Å: Chain B: P.127, T.227, K.228, N.229 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.228, B:N.229

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
A

B
B

17-beta-hydroxysteroid dehydrogenase 13

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