SMTL ID : 5epo.1

The three-dimensional structure of Clostridium absonum 7alpha-hydroxysteroid dehydrogenase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

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

NAP.1: 26 residues within 4Å: Chain A: S.13, T.15, R.16, G.17, I.18, R.38, L.42, F.62, N.63, A.64, R.65, N.90, Y.91, G.92, I.143, Y.158, K.162, P.188, G.189, L.190, I.191, T.193, R.194, A.195, A.196 Ligands: TUD.2 34 PLIP interactions: 34 interactions with chain A Hydrophobic interactions: A:I.18, A:P.188, A:I.191 Hydrogen bonds: A:S.13, A:T.15, A:T.15, A:R.16, A:I.18, A:R.38, A:N.63, A:A.64, A:R.65, A:N.90, A:G.92, A:K.162, A:I.191, A:I.191, A:R.194, A:A.195, A:A.196 Water bridges: A:G.19, A:R.38, A:R.38, A:R.38, A:N.63, A:N.90, A:R.194 Salt bridges: A:R.16, A:R.38, A:R.194, A:R.194 pi-Stacking: A:Y.91, A:Y.91 pi-Cation interactions: A:R.38 NAP.4: 26 residues within 4Å: Chain B: S.13, S.14, T.15, R.16, G.17, I.18, R.38, L.42, F.62, N.63, A.64, R.65, N.90, Y.91, G.92, I.143, Y.158, K.162, P.188, G.189, I.191, T.193, R.194, A.195, A.196 Ligands: TUD.5 32 PLIP interactions: 32 interactions with chain B Hydrophobic interactions: B:I.18, B:P.188, B:I.191 Hydrogen bonds: B:T.15, B:T.15, B:R.16, B:I.18, B:R.38, B:N.63, B:A.64, B:N.90, B:G.92, B:Y.158, B:K.162, B:I.191, B:I.191, B:R.194, B:A.195, B:A.196 Water bridges: B:G.19, B:R.38, B:R.38, B:N.63, B:N.90, B:Y.91, B:R.194 Salt bridges: B:R.16, B:R.38, B:R.194, B:R.194 pi-Stacking: B:Y.91 pi-Cation interactions: B:R.38 NAP.7: 27 residues within 4Å: Chain C: S.13, T.15, R.16, G.17, I.18, R.38, L.42, F.62, N.63, A.64, N.90, Y.91, G.92, I.143, S.144, T.145, Y.158, K.162, P.188, G.189, L.190, I.191, T.193, R.194, A.195, A.196 Ligands: TUD.8 34 PLIP interactions: 34 interactions with chain C Hydrophobic interactions: C:P.188 Hydrogen bonds: C:T.15, C:T.15, C:R.16, C:I.18, C:R.38, C:N.63, C:A.64, C:N.90, C:G.92, C:Y.158, C:K.162, C:I.191, C:I.191, C:T.193, C:T.193, C:R.194, C:A.195, C:A.196 Water bridges: C:S.13, C:G.17, C:G.19, C:R.38, C:R.38, C:N.90, C:R.194, C:R.194, C:R.194 Salt bridges: C:R.16, C:R.38, C:R.194, C:R.194 pi-Stacking: C:Y.91 pi-Cation interactions: C:R.38 NAP.10: 26 residues within 4Å: Chain D: S.13, T.15, R.16, G.17, I.18, R.38, L.42, F.62, N.63, A.64, R.65, N.90, Y.91, G.92, I.143, S.144, Y.158, K.162, G.189, L.190, I.191, T.193, R.194, A.195, A.196 Ligands: TUD.11 33 PLIP interactions: 33 interactions with chain D Hydrophobic interactions: D:A.195 Hydrogen bonds: D:T.15, D:T.15, D:R.16, D:I.18, D:R.38, D:N.63, D:A.64, D:R.65, D:N.90, D:Y.158, D:K.162, D:K.162, D:I.191, D:I.191, D:T.193, D:T.193, D:R.194, D:A.195 Water bridges: D:S.13, D:R.16, D:G.17, D:R.38, D:R.38, D:N.63, D:N.90 Salt bridges: D:R.16, D:R.38, D:R.194, D:R.194 pi-Stacking: D:Y.91, D:Y.91 pi-Cation interactions: D:R.38

4 x TUD: TAUROCHENODEOXYCHOLIC ACID(Non-covalent)

TUD.2: 17 residues within 4Å: Chain A: G.93, T.94, V.96, T.145, G.147, D.152, R.155, Y.158, P.188, G.189, L.190, A.195, A.196, N.199, M.200, F.204 Ligands: NAP.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:V.96, A:Y.158, A:L.190, A:A.196, A:N.199, A:F.204 Hydrogen bonds: A:T.94, A:T.145, A:T.145, A:D.152, A:D.152, A:Y.158 Water bridges: A:R.155, A:N.199 TUD.5: 17 residues within 4Å: Chain B: G.93, T.94, V.96, T.145, I.146, G.147, D.152, R.155, Y.158, G.189, L.190, A.195, A.196, N.199, M.200, F.204 Ligands: NAP.4 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:V.96, B:I.146, B:L.190, B:A.196, B:N.199, B:F.204 Hydrogen bonds: B:T.94, B:T.145, B:T.145, B:D.152, B:D.152 Water bridges: B:R.155 TUD.8: 18 residues within 4Å: Chain C: G.93, T.94, V.96, T.145, I.146, G.147, D.152, R.155, Y.158, P.188, G.189, A.195, A.196, N.199, M.200, F.204, F.208 Ligands: NAP.7 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:V.96, C:I.146, C:Y.158, C:A.195, C:A.196, C:N.199, C:F.204, C:F.208 Hydrogen bonds: C:T.94, C:T.145, C:D.152 Water bridges: C:R.155, C:N.199 TUD.11: 20 residues within 4Å: Chain D: G.93, T.94, N.95, V.96, T.145, I.146, G.147, D.152, R.155, Y.158, P.188, G.189, L.190, A.195, A.196, N.199, M.200, F.204, F.208 Ligands: NAP.10 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:V.96, D:I.146, D:Y.158, D:L.190, D:A.196, D:N.199, D:F.204, D:F.208 Hydrogen bonds: D:T.94, D:T.145, D:T.145, D:D.152, D:D.152 Water bridges: D:V.96, D:R.155

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 10 residues within 4Å: Chain A: K.7, D.85, I.86, G.137, G.138, S.139, R.182, A.231, S.232, D.233 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.7, A:R.182, A:D.233 Water bridges: A:G.138, A:G.138, A:N.180 GOL.6: 10 residues within 4Å: Chain B: K.7, D.85, I.86, G.137, G.138, S.139, R.182, A.231, S.232, D.233 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.7, B:G.138, B:R.182, B:D.233 Water bridges: B:D.85, B:G.138, B:N.180 GOL.9: 10 residues within 4Å: Chain C: K.7, D.85, I.86, G.137, G.138, S.139, R.182, A.231, S.232, D.233 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.182, C:D.233 Water bridges: C:G.138, C:N.180, C:N.180 GOL.12: 9 residues within 4Å: Chain D: D.85, I.86, G.137, G.138, S.139, R.182, A.231, S.232, D.233 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:G.138, D:R.182, D:S.232 Water bridges: D:G.138

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lou, D. et al., The three-dimensional structure of Clostridium absonum 7 alpha-hydroxysteroid dehydrogenase: new insights into the conserved arginines for NADP(H) recognition. Sci Rep (2016)

Release Date

2016-03-23

Peptides

7-alpha-hydroxysteroid deydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

7-alpha-hydroxysteroid deydrogenase