SMTL ID : 2b8j.1

Crystal structure of AphA class B acid phosphatase/phosphotransferase ternary complex with adenosine and phosphate at 2 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.03 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, S.167 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.43, A:D.45, A:D.166, H2O.1, H2O.4, H2O.4 MG.6: 4 residues within 4Å: Chain B: D.43, D.45, T.47, D.166 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.43, B:D.45, B:D.166, H2O.6, H2O.6, H2O.6 MG.8: 5 residues within 4Å: Chain C: D.43, D.45, T.47, D.166, S.167 6 PLIP interactions: 3 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.43, C:D.45, C:D.166, H2O.9, H2O.12, H2O.13 MG.13: 4 residues within 4Å: Chain D: D.43, D.45, T.47, D.166 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.43, D:D.45, D:D.166, H2O.14, H2O.14, H2O.14

2 x SPM: SPERMINE(Non-covalent)

SPM.2: 12 residues within 4Å: Chain A: D.45, F.55, W.56, K.59, Y.69, G.112, R.113, D.144, T.191, Y.192 Ligands: PO4.3, AU.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.55, A:F.55, A:W.56, A:K.59, A:Y.192 Hydrogen bonds: A:Y.69, A:G.112, A:T.191 SPM.9: 12 residues within 4Å: Chain C: D.45, F.55, W.56, K.59, Y.69, G.112, R.113, D.144, T.191, Y.192 Ligands: PO4.10, AU.11 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.55, C:F.55, C:W.56, C:K.59, C:Y.192 Hydrogen bonds: C:G.112

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

PO4.3: 8 residues within 4Å: Chain A: D.43, T.111, G.112, D.144, K.151, N.169, D.170 Ligands: SPM.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.43, A:D.43, A:T.111, A:G.112, A:N.169 Water bridges: A:I.44, A:D.45 Salt bridges: A:K.151 PO4.10: 8 residues within 4Å: Chain C: D.43, T.111, G.112, D.144, K.151, N.169, D.170 Ligands: SPM.9 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:D.43, C:D.43, C:G.112, C:N.169 Water bridges: C:D.45, C:D.45, C:D.45 Salt bridges: C:K.151

2 x AU: GOLD ION(Non-covalent)

AU.4: 2 residues within 4Å: Chain A: Y.192 Ligands: SPM.2 No protein-ligand interaction detected (PLIP) AU.11: 2 residues within 4Å: Chain C: Y.192 Ligands: SPM.9 No protein-ligand interaction detected (PLIP)

2 x AU3: GOLD 3+ ION(Non-functional Binders)

AU3.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) AU3.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x ADN: ADENOSINE(Non-covalent)

ADN.7: 10 residues within 4Å: Chain B: D.45, S.52, F.55, Y.69, L.70, W.76, G.112, R.113, T.191, Y.192 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:D.45, B:Y.69, B:G.112, B:T.191, B:T.191 Water bridges: B:G.112, B:K.151 pi-Stacking: B:F.55, B:Y.192 ADN.14: 10 residues within 4Å: Chain D: D.45, S.52, F.55, Y.69, L.70, W.76, G.112, R.113, T.191, Y.192 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:Y.69, D:G.112, D:T.191 Water bridges: D:G.112, D:K.151, D:T.191 pi-Stacking: D:F.55, 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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