SMTL ID : 4is3.1

Crystal structure of a 3alpha-hydroxysteroid dehydrogenase (BaiA2) associated with secondary bile acid synthesis from Clostridium scindens VPI12708 in complex with a putative NAD(+)-OH- adduct at 2.0 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 28 residues within 4Å: Chain A: G.32, G.33, T.34, R.35, G.36, I.37, E.57, E.61, L.85, N.111, A.112, G.113, I.114, I.134, T.161, A.162, S.163, Y.176, K.180, P.206, G.207, V.208, V.209, T.211, D.212, M.213, T.214 Ligands: UNL.2 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:P.206 Hydrogen bonds: A:G.32, A:T.34, A:R.35, A:R.35, A:I.37, A:E.57, A:E.61, A:N.111, A:G.113, A:I.114, A:K.180, A:V.209, A:V.209, A:D.212 Water bridges: A:R.35, A:R.35, A:R.35, A:R.35, A:G.36, A:G.38, A:E.57, A:E.57, A:E.57, A:E.57, A:E.57, A:N.111, A:H.130, A:D.212 Salt bridges: A:R.35 NAD.4: 28 residues within 4Å: Chain B: G.32, G.33, T.34, R.35, G.36, I.37, E.57, E.61, L.85, N.111, A.112, G.113, I.114, I.134, T.161, A.162, S.163, Y.176, K.180, P.206, G.207, V.208, V.209, T.211, D.212, M.213, T.214 Ligands: UNL.5 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:P.206 Hydrogen bonds: B:G.32, B:T.34, B:T.34, B:R.35, B:R.35, B:I.37, B:E.57, B:E.61, B:N.111, B:G.113, B:I.114, B:K.180, B:V.209, B:V.209, B:T.211, B:D.212 Water bridges: B:R.35, B:R.35, B:R.35, B:G.38, B:E.57, B:E.57, B:E.57, B:E.57, B:N.111, B:T.161 Salt bridges: B:R.35 NAD.7: 29 residues within 4Å: Chain C: G.32, G.33, T.34, R.35, G.36, I.37, G.56, E.57, E.61, L.85, N.111, A.112, G.113, I.114, I.134, T.161, A.162, S.163, Y.176, K.180, P.206, G.207, V.208, V.209, T.211, D.212, M.213, T.214 Ligands: UNL.8 28 PLIP interactions: 28 interactions with chain C Hydrophobic interactions: C:P.206 Hydrogen bonds: C:G.32, C:T.34, C:R.35, C:R.35, C:I.37, C:E.57, C:E.61, C:N.111, C:G.113, C:I.114, C:K.180, C:V.209, C:V.209, C:D.212 Water bridges: C:R.35, C:R.35, C:R.35, C:R.35, C:G.36, C:G.38, C:E.57, C:D.84, C:N.111, C:H.130, C:T.161, C:D.212 Salt bridges: C:R.35 NAD.9: 27 residues within 4Å: Chain D: G.32, G.33, T.34, R.35, G.36, I.37, E.57, E.61, L.85, N.111, A.112, G.113, I.114, I.134, T.161, A.162, S.163, Y.176, K.180, P.206, G.207, V.208, V.209, T.211, M.213, T.214 Ligands: UNL.10 25 PLIP interactions: 25 interactions with chain D Hydrophobic interactions: D:P.206 Hydrogen bonds: D:G.32, D:T.34, D:T.34, D:R.35, D:R.35, D:I.37, D:E.57, D:E.61, D:N.111, D:G.113, D:I.114, D:K.180, D:V.209, D:V.209, D:T.211, D:D.212 Water bridges: D:R.35, D:G.38, D:E.57, D:E.57, D:N.111, D:H.130, D:D.212 Salt bridges: D:R.35

4 x UNL: UNKNOWN LIGAND

UNL.2: 5 residues within 4Å: Chain A: A.162, S.163, Y.176, K.180 Ligands: NAD.1 No protein-ligand interaction detected (PLIP) UNL.5: 4 residues within 4Å: Chain B: S.163, Y.176, K.180 Ligands: NAD.4 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.163, B:S.163, B:Y.176 UNL.8: 4 residues within 4Å: Chain C: S.163, Y.176, K.180 Ligands: NAD.7 No protein-ligand interaction detected (PLIP) UNL.10: 5 residues within 4Å: Chain D: A.162, S.163, Y.176, K.180 Ligands: NAD.9 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.176

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

ACT.3: 4 residues within 4Å: Chain A: T.34, R.35, E.61, T.64 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.64 Hydrogen bonds: A:T.34 Salt bridges: A:R.35 ACT.6: 4 residues within 4Å: Chain B: T.34, R.35, E.61, T.64 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.64 Water bridges: B:E.61 Salt bridges: B:R.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of a 3alpha-hydroxysteroid dehydrogenase (BaiA2) associated with secondary bile acid synthesis from Clostridium scindens VPI12708 in complex with a putative NAD(+)-OH- adduct at 2.0 A resolution. To be published

Release Date

2013-04-24

Peptides

Bile acid 3-alpha hydroxysteroid dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Bile acid 3-alpha hydroxysteroid dehydrogenase

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