SMTL ID : 4n3v.2 (1 other biounit)

Crystal structure of a bile-acid 7-alpha dehydratase (CLOHIR_00079) from Clostridium hiranonis DSM 13275 at 1.89 A resolution with product added

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-trimer

Ligands

3 x UNL: UNKNOWN LIGAND

UNL.1: 8 residues within 4Å: Chain A: Y.49, G.76, K.77, F.80, V.86, Y.89, L.90, T.161 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.49, A:G.76, A:Y.89, A:Y.89 UNL.5: 8 residues within 4Å: Chain B: Y.49, G.76, K.77, F.80, V.86, Y.89, L.90, T.161 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.49, B:G.76, B:Y.89, B:Y.89 UNL.9: 8 residues within 4Å: Chain C: Y.49, G.76, K.77, F.80, V.86, Y.89, L.90, T.161 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.49, C:G.76, C:Y.89, C:Y.89

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.105 Chain B: H.105 Chain C: H.105 Ligands: ZN.6, ZN.10 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:H.105, C:H.105, B:H.105, H2O.1, H2O.5, H2O.9 ZN.6: 5 residues within 4Å: Chain A: H.105 Chain B: H.105 Chain C: H.105 Ligands: ZN.2, ZN.10 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:H.105, C:H.105, B:H.105, H2O.1, H2O.5, H2O.9 ZN.10: 5 residues within 4Å: Chain A: H.105 Chain B: H.105 Chain C: H.105 Ligands: ZN.2, ZN.6 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:H.105, C:H.105, B:H.105, H2O.1, H2O.5, H2O.9

3 x NA: SODIUM ION(Non-functional Binders)

NA.3: 5 residues within 4Å: Chain A: E.124 Chain B: E.124 Chain C: E.124 Ligands: NA.7, NA.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.124 NA.7: 5 residues within 4Å: Chain A: E.124 Chain B: E.124 Chain C: E.124 Ligands: NA.3, NA.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.124 NA.11: 5 residues within 4Å: Chain A: E.124 Chain B: E.124 Chain C: E.124 Ligands: NA.3, NA.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.124

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

CIT.4: 12 residues within 4Å: Chain A: K.43, T.106, P.107 Chain B: K.43, T.106, P.107, W.121 Chain C: K.43, P.107, W.121 Ligands: CIT.8, CIT.12 9 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C, 4 interactions with chain B Water bridges: A:T.106 Salt bridges: A:K.43, A:K.43, C:K.43, B:K.43, B:K.43 Hydrophobic interactions: C:P.107, B:P.107 Hydrogen bonds: B:T.106 CIT.8: 12 residues within 4Å: Chain A: K.43, P.107, W.121 Chain B: K.43, T.106, P.107 Chain C: K.43, T.106, P.107, W.121 Ligands: CIT.4, CIT.12 9 PLIP interactions: 2 interactions with chain A, 4 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: A:P.107, C:P.107 Salt bridges: A:K.43, C:K.43, C:K.43, B:K.43, B:K.43 Hydrogen bonds: C:T.106 Water bridges: B:T.106 CIT.12: 12 residues within 4Å: Chain A: K.43, T.106, P.107, W.121 Chain B: K.43, P.107, W.121 Chain C: K.43, T.106, P.107 Ligands: CIT.4, CIT.8 9 PLIP interactions: 4 interactions with chain A, 3 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: A:P.107, B:P.107 Hydrogen bonds: A:T.106 Salt bridges: A:K.43, A:K.43, C:K.43, C:K.43, B:K.43 Water bridges: C:T.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of a bile-acid 7-alpha dehydratase (CLOHIR_00079) from Clostridium hiranonis DSM 13275 at 1.89 A resolution with product added. To be published

Release Date

2013-12-04

Peptides

Bile acid 7-alpha dehydratase, BaiE: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
B

Bile acid 7-alpha dehydratase, BaiE

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