SMTL ID : 7c83.1

Crystal structure of an integral membrane steroid 5-alpha-reductase PbSRD5A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.1: 27 residues within 4Å: Chain A: Y.37, G.38, R.39, W.55, R.95, F.99, M.103, R.104, V.105, N.164, D.168, L.171, L.174, R.175, R.181, Y.182, E.183, N.197, Y.198, E.201, T.224, N.227, L.228, R.231, H.235, Y.239 Ligands: OLC.2 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:L.228 Hydrogen bonds: A:Y.37, A:R.39, A:N.164, A:D.168, A:Y.182, A:Y.182, A:E.183, A:N.197, A:N.197, A:Y.198, A:E.201, A:T.224, A:N.227, A:Y.239, A:Y.239 Water bridges: A:R.39, A:R.39, A:R.95, A:R.104, A:R.231, A:R.231 Salt bridges: A:R.175, A:H.235 pi-Stacking: A:Y.182

8 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLC.2: 19 residues within 4Å: Chain A: F.22, S.26, T.29, L.30, V.33, Y.37, W.45, A.54, W.55, Q.58, E.59, T.110, T.114, A.115, A.118, F.121, F.223, N.227 Ligands: NDP.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.22, A:L.30, A:V.33, A:W.45, A:W.55, A:F.121, A:F.223, A:F.223 Hydrogen bonds: A:Q.58 Water bridges: A:W.55, A:A.115 OLC.3: 12 residues within 4Å: Chain A: G.86, L.90, L.93, Q.94, V.98, W.161, L.165, A.169, R.172, R.173 Ligands: OLC.4, OLC.9 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.90, A:L.93, A:L.93, A:Q.94, A:W.161, A:L.165 Hydrogen bonds: A:R.172 Water bridges: A:R.172 Salt bridges: A:R.172 OLC.4: 4 residues within 4Å: Chain A: L.102, R.104, R.172 Ligands: OLC.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.104, A:R.104, A:R.172 OLC.5: 8 residues within 4Å: Chain A: V.203, C.206, A.209, L.210, W.213, T.214, Y.215, A.218 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.203, A:A.209, A:W.213 Hydrogen bonds: A:Y.215 OLC.6: 2 residues within 4Å: Chain A: G.159, A.162 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.162 OLC.7: 7 residues within 4Å: Chain A: L.53, A.54, A.57, L.112, A.115, L.116, F.119 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.53, A:L.112, A:A.115, A:F.119, A:F.119 OLC.8: 8 residues within 4Å: Chain A: L.83, G.86, L.87, L.145, A.146, F.150, A.151, A.154 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.87, A:L.145, A:F.150, A:A.151, A:A.154 OLC.9: 5 residues within 4Å: Chain A: W.161, H.166, A.169, R.173 Ligands: OLC.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.161 Hydrogen bonds: A:R.173, A:R.173

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Han, Y. et al., Crystal structure of steroid reductase SRD5A reveals conserved steroid reduction mechanism. Nat Commun (2021)

Release Date

2021-01-27

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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3-oxo-5-alpha-steroid 4-dehydrogenase