SMTL ID : 2b82.1

Crystal structure of AphA class B acid phosphatase/phosphotransferase ternary complex with adenosine and phosphate bound to the catalytic metal at 1.2 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.43, D.45, T.47, D.166 Ligands: PO4.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.43, A:D.45, A:D.166, H2O.17, H2O.17 MG.4: 4 residues within 4Å: Chain B: D.43, D.45, D.166 Ligands: PO4.5 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.43, B:D.45, B:D.166, H2O.33, H2O.33 MG.7: 5 residues within 4Å: Chain C: D.43, D.45, T.47, D.166 Ligands: PO4.8 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.43, C:D.45, C:D.166, H2O.50, H2O.50 MG.10: 4 residues within 4Å: Chain D: D.43, D.45, D.166 Ligands: PO4.11 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.43, D:D.45, D:D.166, H2O.66, H2O.66

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

PO4.2: 8 residues within 4Å: Chain A: D.43, I.44, D.45, T.111, G.112, K.151 Ligands: MG.1, ADN.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:I.44, A:D.45, A:D.45, A:D.45, A:T.111, A:T.111, A:G.112 Salt bridges: A:K.151 PO4.5: 9 residues within 4Å: Chain B: D.43, I.44, D.45, T.111, G.112, R.113, K.151 Ligands: MG.4, ADN.6 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:I.44, B:D.45, B:T.111, B:T.111, B:G.112, B:R.113 Water bridges: B:S.167 Salt bridges: B:K.151 PO4.8: 8 residues within 4Å: Chain C: D.43, I.44, D.45, T.111, G.112, K.151 Ligands: MG.7, ADN.9 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:I.44, C:D.45, C:D.45, C:T.111, C:G.112 Water bridges: C:D.144 Salt bridges: C:K.151 PO4.11: 9 residues within 4Å: Chain D: D.43, I.44, D.45, T.111, G.112, R.113, K.151 Ligands: MG.10, ADN.12 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:I.44, D:D.45, D:D.45, D:T.111, D:G.112, D:R.113 Water bridges: D:S.167 Salt bridges: D:K.151

4 x ADN: ADENOSINE(Non-covalent)

ADN.3: 10 residues within 4Å: Chain A: F.55, Y.69, L.70, W.76, G.112, R.113, D.144, T.191, Y.192 Ligands: PO4.2 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:Y.69, A:G.112, A:G.112, A:T.191, A:T.191 Water bridges: A:D.43, A:L.70, A:D.144, A:D.144, A:S.167, A:S.167, A:Y.192 pi-Stacking: A:Y.192 ADN.6: 9 residues within 4Å: Chain B: F.55, Y.69, L.70, W.76, G.112, R.113, T.191, Y.192 Ligands: PO4.5 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:Y.69, B:G.112, B:T.191, B:T.191 Water bridges: B:D.43, B:L.70, B:D.144, B:D.144, B:S.167, B:Y.192, B:Y.192 pi-Stacking: B:Y.192 ADN.9: 10 residues within 4Å: Chain C: F.55, Y.69, L.70, W.76, G.112, R.113, D.144, T.191, Y.192 Ligands: PO4.8 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:G.112, C:G.112, C:D.144, C:T.191 Water bridges: C:D.43, C:L.70, C:D.144, C:D.144, C:S.167, C:S.167, C:Y.192 pi-Stacking: C:Y.192 ADN.12: 9 residues within 4Å: Chain D: F.55, Y.69, L.70, W.76, G.112, R.113, T.191, Y.192 Ligands: PO4.11 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:Y.69, D:G.112, D:T.191 Water bridges: D:D.43, D:L.70, D:K.71, D:D.144, D:S.167, D:T.191, D:Y.192, D:Y.192 pi-Stacking: D:Y.192

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Calderone, V. et al., A structure-based proposal for the catalytic mechanism of the bacterial acid phosphatase AphA belonging to the DDDD superfamily of phosphohydrolases. J.Mol.Biol. (2006)

Release Date

2005-11-29

Peptides

class B acid phosphatase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

class B acid phosphatase

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