SMTL ID : 1xjb.1

Crystal structure of human type 3 3alpha-hydroxysteroid dehydrogenase in complex with NADP(H), citrate and acetate molecules

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 10 residues within 4Å: Chain A: Y.7, Q.8, P.19, V.20, L.21, G.47, F.48, H.49, H.50, F.286 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.7, A:F.286 Hydrogen bonds: A:Q.8, A:V.20, A:L.21, A:H.49, A:H.50 ACT.2: 4 residues within 4Å: Chain A: Y.57, H.119 Ligands: NAP.3, CIT.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.57 Salt bridges: A:H.119 ACT.7: 3 residues within 4Å: Chain B: Y.57, H.119 Ligands: NAP.10 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.119

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

NAP.3: 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, L.238, A.255, L.270, A.271, K.272, S.273, Y.274, N.275, R.278, Q.281, N.282 Ligands: ACT.2 28 PLIP interactions: 28 interactions with chain A Hydrogen bonds: A:T.25, A:Y.26, A:D.52, A:S.168, A:N.169, A:Q.192, A:S.219, A:L.221, A:S.223, A:H.224, A:K.272, A:K.272, A:S.273, 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, 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.10: 29 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, R.278, Q.281, N.282, L.308 Ligands: ACT.7 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:L.308 Hydrogen bonds: B:T.25, B:Y.26, B:Y.26, B:D.52, B:D.52, B:Y.57, 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:S.273, B:Y.274, B:Q.281, B:N.282, B:N.282 Water bridges: B:A.220, B:A.220, B:T.253 Salt bridges: B:H.224, B:K.272, B:R.278 pi-Stacking: B:Y.218 pi-Cation interactions: B:R.278

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

EDO.4: 4 residues within 4Å: Chain A: K.125, F.141, D.142, T.143 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.125, A:F.141, A:T.143 Water bridges: A:R.93 EDO.11: 10 residues within 4Å: Chain B: Y.7, Q.8, P.19, V.20, L.21, G.47, F.48, H.49, H.50, F.286 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.8, B:V.20, B:L.21, B:H.49, B:H.50

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.5: 8 residues within 4Å: Chain A: Y.26, V.56, W.88, H.224, E.226, W.229, L.308 Ligands: ACT.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.229, A:W.229 Hydrogen bonds: A:Y.26 Salt bridges: A:H.224

1 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.6: 5 residues within 4Å: Chain A: K.6, Y.7, C.9 Chain B: S.5, Y.7 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.5

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

SO4.8: 1 residues within 4Å: Chain B: R.278 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.278 SO4.9: 1 residues within 4Å: Chain B: R.93 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.93, B:R.93, B:R.93 Salt bridges: B:R.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Couture, J.-F. et al., Comparison of crystal structures of human type 3 3alpha-hydroxysteroid dehydrogenase reveals an "induced-fit" mechanism and a conserved basic motif involved in the binding of androgen. Protein Sci. (2005)

Release Date

2005-06-21

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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