SMTL ID : 8g9v.4 (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 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:P.219 Hydrogen bonds: A:G.46, A:G.46, A:I.49, A:G.50, 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, A:T.224 Salt bridges: A:H.47 NAD.5: 27 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, P.219, V.220, F.221, V.222, T.224, F.226 Ligands: YYC.6 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:P.219 Hydrogen bonds: B:G.46, B:I.49, B:I.69, B:D.94, B:C.95, B:S.96, B:N.121, B:N.121, B:V.222, B:V.222 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: 15 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, I.264, F.267, L.268, Q.271 Ligands: NAD.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.174, A:V.174, A:V.220, A:F.221, A:F.221, A:F.267 Hydrogen bonds: A:S.173, A:Y.186, A:Y.186, A:F.221 YYC.6: 19 residues within 4Å: Chain B: S.173, V.174, C.175, E.178, I.180, L.183, Y.186, P.219, V.220, F.221, F.226, W.235, I.264, F.267, L.268, Q.271, L.282, F.290 Ligands: NAD.5 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:V.174, B:V.174, B:V.174, B:E.178, B:I.180, B:V.220, B:F.221, B:W.235, B:F.267, B:F.267, B:L.282 Hydrogen bonds: B:S.173, B:Y.186, B:Y.186, B:F.221 pi-Stacking: B:W.235

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

SO4.3: 4 residues within 4Å: Chain A: E.21, K.255, K.256, M.257 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.256, A:M.257, A:M.257 Salt bridges: A:K.255 SO4.4: 4 residues within 4Å: Chain A: T.14, R.269 Chain B: R.269, K.272 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.269, B:K.272 SO4.7: 5 residues within 4Å: Chain A: K.272 Chain B: K.255, K.256, M.257 Ligands: SO4.9 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.256, B:M.257 Salt bridges: B:K.255, B:K.256, A:K.272 SO4.8: 1 residues within 4Å: Chain B: R.277 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.277 SO4.9: 4 residues within 4Å: Chain A: K.272 Chain B: R.198, M.257 Ligands: SO4.7 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.198

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
G

B
H

Membrane

We predict this structure to be a membrane protein.
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17-beta-hydroxysteroid dehydrogenase 13

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