SMTL ID : 3o0f.1

Crystal structure of a putative metal-dependent phosphoesterase (BAD_1165) from bifidobacterium adolescentis atcc 15703 at 1.94 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

monomer

Ligands

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 15 residues within 4Å: Chain A: D.25, H.86, R.110, R.113, G.145, R.146, P.147, R.162, S.163, F.166, H.263, G.266, K.267 Ligands: PO4.5, EDO.7 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:R.146, A:R.162, A:G.266, A:K.267 Water bridges: A:R.146, A:R.162 Salt bridges: A:R.110, A:R.113, A:R.146 pi-Stacking: A:F.166 pi-Cation interactions: A:K.267

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.20, D.25, H.50, H.263 Ligands: PO4.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.25, A:D.25, A:H.50, A:H.263

2 x FE: FE (III) ION(Non-covalent)

FE.3: 5 residues within 4Å: Chain A: E.75, H.86, H.203 Ligands: FE.4, PO4.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.75, A:H.86, A:H.203, H2O.7 FE.4: 6 residues within 4Å: Chain A: H.18, H.20, E.75, D.261 Ligands: FE.3, PO4.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.18, A:H.20, A:E.75, A:D.261, H2O.7

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 12 residues within 4Å: Chain A: H.20, D.25, H.50, E.75, H.86, D.261, H.263, K.267 Ligands: AMP.1, ZN.2, FE.3, FE.4 5 PLIP interactions: 5 interactions with chain A Salt bridges: A:H.20, A:H.50, A:H.86, A:H.263, A:K.267

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

EDO.6: 4 residues within 4Å: Chain A: Q.36, W.262, G.270, L.271 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.36, A:L.271 EDO.7: 10 residues within 4Å: Chain A: S.24, D.25, H.50, R.110, T.143, I.144, G.145, P.147, H.148 Ligands: AMP.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.110, A:R.110, A:T.143

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Han, G.W. et al., Crystal structure of a metal-dependent phosphoesterase (YP_910028.1) from Bifidobacterium adolescentis: Computational prediction and experimental validation of phosphoesterase activity. Proteins (2011)

Release Date

2010-08-25

Peptides

putative metal-dependent phosphoesterase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

putative metal-dependent phosphoesterase

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