SMTL ID : 3qfo.1

Crystal structure of Streptococcal asymmetric Ap4A hydrolase and phosphodiesterase Spr1479/SapH im complex with AMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 14 residues within 4Å: Chain A: H.21, D.47, N.74, W.75, R.145, I.148, H.149, H.172, I.173, H.174, F.197, H.260 Ligands: FE.2, MN.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:W.75, A:R.145, A:H.149, A:H.174, A:H.260 Water bridges: A:H.149 Salt bridges: A:H.21, A:H.172, A:H.174 AMP.4: 14 residues within 4Å: Chain B: H.21, D.47, N.74, W.75, R.145, I.148, H.149, H.172, I.173, H.174, F.197, H.260 Ligands: FE.5, MN.6 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.74, B:W.75, B:R.145, B:H.149, B:H.174, B:H.260 Salt bridges: B:H.21, B:H.172, B:H.174

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

FE.2: 6 residues within 4Å: Chain A: D.19, H.21, D.47, H.174 Ligands: AMP.1, MN.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.19, A:H.21, A:D.47, A:H.174, AMP.1 FE.5: 6 residues within 4Å: Chain B: D.19, H.21, D.47, H.174 Ligands: AMP.4, MN.6 6 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: B:D.19, B:H.21, B:D.47, B:H.174, AMP.4, H2O.6

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.3: 7 residues within 4Å: Chain A: D.19, D.47, N.74, H.136, H.172 Ligands: AMP.1, FE.2 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.47, A:H.136, A:H.172, H2O.1, AMP.1 MN.6: 7 residues within 4Å: Chain B: D.19, D.47, N.74, H.136, H.172 Ligands: AMP.4, FE.5 5 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: B:D.47, B:H.136, B:H.172, AMP.4, H2O.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jiang, Y.L. et al., Structural and enzymatic characterization of a Streptococcal ATP/diadenosine polyphosphate and phosphodiester hydrolase Spr1479/SapH. To be Published

Release Date

2011-08-24

Peptides

Putative uncharacterized protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Putative uncharacterized protein

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