SMTL ID : 4l8o.1

Crystal structure of a bile-acid 7-alpha dehydratase (CLOHYLEM_06634) from Clostridium hylemonae DSM 15053 at 2.20 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-trimer

Ligands

3 x CO: COBALT (II) ION(Non-covalent)

CO.1: 5 residues within 4Å: Chain A: H.105 Chain B: H.105 Chain C: H.105 Ligands: CO.8, CO.15 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.3, H2O.6 CO.8: 5 residues within 4Å: Chain A: H.105 Chain B: H.105 Chain C: H.105 Ligands: CO.1, CO.15 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.3, H2O.6 CO.15: 5 residues within 4Å: Chain A: H.105 Chain B: H.105 Chain C: H.105 Ligands: CO.1, CO.8 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.3, H2O.6

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

NA.2: 5 residues within 4Å: Chain A: E.124 Chain B: E.124 Chain C: E.124 Ligands: NA.9, NA.16 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.124 NA.9: 5 residues within 4Å: Chain A: E.124 Chain B: E.124 Chain C: E.124 Ligands: NA.2, NA.16 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.124 NA.16: 5 residues within 4Å: Chain A: E.124 Chain B: E.124 Chain C: E.124 Ligands: NA.2, NA.9 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.124

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

SO4.3: 8 residues within 4Å: Chain A: K.43, P.107 Chain B: K.43, P.107 Chain C: K.43, P.107 Ligands: SO4.10, SO4.17 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C Salt bridges: B:K.43, A:K.43, C:K.43 SO4.10: 8 residues within 4Å: Chain A: K.43, P.107 Chain B: K.43, P.107 Chain C: K.43, P.107 Ligands: SO4.3, SO4.17 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C Salt bridges: B:K.43, A:K.43, C:K.43 SO4.17: 8 residues within 4Å: Chain A: K.43, P.107 Chain B: K.43, P.107 Chain C: K.43, P.107 Ligands: SO4.3, SO4.10 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B Salt bridges: A:K.43, C:K.43, B:K.43

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

EDO.4: 3 residues within 4Å: Chain A: S.138, V.140, H.171 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.138, A:H.171 EDO.5: 5 residues within 4Å: Chain A: T.147, K.149, E.161, T.162, G.163 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.163 EDO.6: 4 residues within 4Å: Chain A: T.71, S.72, Y.73, Y.89 No protein-ligand interaction detected (PLIP) EDO.7: 5 residues within 4Å: Chain A: R.174, I.178 Chain C: N.141, E.170, F.172 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:N.141, C:E.170, A:R.174 EDO.11: 3 residues within 4Å: Chain B: S.138, V.140, H.171 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.138, B:H.171 EDO.12: 5 residues within 4Å: Chain B: T.147, K.149, E.161, T.162, G.163 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.163 EDO.13: 4 residues within 4Å: Chain B: T.71, S.72, Y.73, Y.89 No protein-ligand interaction detected (PLIP) EDO.14: 5 residues within 4Å: Chain A: N.141, E.170, F.172 Chain B: R.174, I.178 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.141, A:E.170, B:R.174 EDO.18: 3 residues within 4Å: Chain C: S.138, V.140, H.171 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.138, C:H.171 EDO.19: 5 residues within 4Å: Chain C: T.147, K.149, E.161, T.162, G.163 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.163 EDO.20: 4 residues within 4Å: Chain C: T.71, S.72, Y.73, Y.89 No protein-ligand interaction detected (PLIP) EDO.21: 5 residues within 4Å: Chain B: N.141, E.170, F.172 Chain C: R.174, I.178 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:N.141, B:E.170, C:R.174

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 (CLOHYLEM_06634) from Clostridium hylemonae DSM 15053 at 2.20 A resolution. To be published

Release Date

2013-08-21

Peptides

Bile acid 7a-dehydratase, BaiE: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Bile acid 7a-dehydratase, BaiE