SMTL ID : 4xo6.1

Crystal structure of human 3-alpha hydroxysteroid dehydrogenase type 3 in complex with NADP+, 5alpha-androstan-3,17-dione and (3beta, 5alpha)-3-hydroxyandrostan-17-one

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

homo-dimer

Ligands

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 29 residues within 4Å: Chain A: G.24, T.25, Y.26, D.52, Y.57, K.86, H.119, S.168, N.169, Q.192, Y.218, S.219, A.220, L.221, G.222, S.223, H.224, A.255, L.270, A.271, K.272, S.273, Y.274, N.275, R.278, Q.281, N.282, L.308 Ligands: 5SD.2 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:L.308 Hydrogen bonds: A:T.25, A:Y.26, A:D.52, A:D.52, A:Y.57, A:S.168, A:N.169, A:Q.192, A:S.219, A:L.221, A:G.222, A:S.223, A:H.224, A:K.272, A:Y.274, A:Q.281, A:Q.281, A:N.282 Water bridges: A:A.220, A:A.220, A:H.224, A:K.272, A:R.278 Salt bridges: A:H.224, A:K.272, A:R.278 pi-Stacking: A:Y.218 pi-Cation interactions: A:R.278 NAP.6: 30 residues within 4Å: Chain B: G.24, T.25, Y.26, D.52, Y.57, K.86, H.119, S.168, N.169, Q.192, Y.218, S.219, A.220, L.221, G.222, S.223, H.224, L.238, A.255, L.270, A.271, K.272, S.273, Y.274, N.275, R.278, Q.281, N.282, L.308 Ligands: AOX.7 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:L.308 Hydrogen bonds: B:T.25, B:Y.26, B:D.52, B:S.168, B:N.169, B:Q.192, B:S.219, B:L.221, B:S.223, B:H.224, B:K.272, B:Y.274, B:Q.281, B:N.282, B:N.282 Water bridges: B:Y.57, B:A.220, B:A.220, B:H.224, B:K.272 Salt bridges: B:H.224, B:K.272, B:R.278 pi-Stacking: B:Y.218 pi-Cation interactions: B:R.278

1 x 5SD: 5ALPHA-ANDROSTAN-3,17-DIONE(Non-covalent)

5SD.2: 8 residues within 4Å: Chain A: Y.26, V.56, W.88, H.119, I.131, W.229, L.310 Ligands: NAP.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.26, A:W.88, A:I.131, A:W.229, A:L.310

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

SO4.3: 7 residues within 4Å: Chain A: R.202, K.209, R.265 Chain B: Q.264, S.292, M.295 Ligands: SO4.8 9 PLIP interactions: 2 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:Q.264, A:R.265 Water bridges: B:S.292, A:R.202, A:R.202, A:R.202, A:R.202 Salt bridges: A:R.202, A:K.209 SO4.8: 6 residues within 4Å: Chain A: Q.264, S.292, M.295 Chain B: K.209, R.265 Ligands: SO4.3 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Water bridges: B:D.206, A:T.291 Salt bridges: B:K.209 Hydrogen bonds: A:Q.264

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 5 residues within 4Å: Chain A: K.251, R.252, T.253, L.256, Q.284 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.251, A:Q.284 EDO.9: 5 residues within 4Å: Chain B: K.251, R.252, L.256, Q.281, Q.284 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.251, B:Q.284

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: P.94, E.95, A.152, K.155 2 PLIP interactions: 2 interactions with chain A Water bridges: A:A.152, A:K.155

1 x AOX: (3Beta,5alpha)-3-Hydroxyandrostan-17-one(Non-covalent)

AOX.7: 8 residues within 4Å: Chain B: Y.26, V.56, V.130, I.131, H.224, W.229, L.308 Ligands: NAP.6 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.26, B:V.56, B:V.56, B:V.130, B:I.131, B:W.229 Hydrogen bonds: B:H.224

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, B. et al., Human 3 alpha-hydroxysteroid dehydrogenase type 3: structural clues of 5 alpha-DHT reverse binding and enzyme down-regulation decreasing MCF7 cell growth. Biochem.J. (2016)

Release Date

2016-02-17

Peptides

Aldo-keto reductase family 1 member C2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Aldo-keto reductase family 1 member C2

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