SMTL ID : 4l8p.1

Crystal structure of a bile-acid 7-alpha dehydratase (CLOHIR_00079) from Clostridium hiranonis DSM 13275 at 1.60 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-trimer

Ligands

3 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 5 residues within 4Å: Chain A: H.105 Chain B: H.105 Chain C: H.105 Ligands: NI.5, NI.9 6 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: C:H.105, A:H.105, B:H.105, H2O.1, H2O.6, H2O.11 NI.5: 5 residues within 4Å: Chain A: H.105 Chain B: H.105 Chain C: H.105 Ligands: NI.1, NI.9 6 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: C:H.105, A:H.105, B:H.105, H2O.1, H2O.6, H2O.11 NI.9: 5 residues within 4Å: Chain A: H.105 Chain B: H.105 Chain C: H.105 Ligands: NI.1, NI.5 6 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: C:H.105, A:H.105, B:H.105, H2O.1, H2O.6, H2O.11

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.6, NA.10 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 1 interactions with chain C Water bridges: A:E.124, B:E.124, C:E.124 Hydrogen bonds: B:E.124 NA.6: 5 residues within 4Å: Chain A: E.124 Chain B: E.124 Chain C: E.124 Ligands: NA.2, NA.10 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: A:E.124 Water bridges: A:E.124, B:E.124, C:E.124 NA.10: 5 residues within 4Å: Chain A: E.124 Chain B: E.124 Chain C: E.124 Ligands: NA.2, NA.6 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 1 interactions with chain C Water bridges: A:E.124, B:E.124, C:E.124 Hydrogen bonds: B:E.124

3 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.3: 6 residues within 4Å: Chain A: H.170, F.171, M.172 Chain C: D.174, K.176, I.177 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:D.174 Water bridges: C:D.174, A:H.170 PGE.7: 6 residues within 4Å: Chain A: D.174, K.176, I.177 Chain B: H.170, F.171, M.172 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:H.170, A:D.174 Hydrogen bonds: A:D.174 PGE.11: 6 residues within 4Å: Chain B: D.174, K.176, I.177 Chain C: H.170, F.171, M.172 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Water bridges: C:H.170, B:D.174 Hydrogen bonds: B:D.174

3 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.4: 13 residues within 4Å: Chain A: Y.49, F.50, L.53, Y.73, S.74, D.75, L.78, F.80, L.90, H.102, Y.145, I.158, T.161 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.49 1PE.8: 13 residues within 4Å: Chain B: Y.49, F.50, L.53, Y.73, S.74, D.75, L.78, F.80, L.90, H.102, Y.145, I.158, T.161 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.49 1PE.12: 13 residues within 4Å: Chain C: Y.49, F.50, L.53, Y.73, S.74, D.75, L.78, F.80, L.90, H.102, Y.145, I.158, T.161 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.49

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 1.60 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

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