SMTL ID : 3cz4.1

Native AphA class B acid phosphatase/phosphotransferase from E. coli

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.44, D.46, T.48, D.167, S.168 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.44, A:D.46, A:D.167, H2O.3, H2O.9, H2O.11 MG.4: 9 residues within 4Å: Chain A: A.188, S.189, N.190 Chain B: A.188, S.189, N.190 Ligands: CL.3, CL.12, MG.13 No protein-ligand interaction detected (PLIP) MG.10: 5 residues within 4Å: Chain B: D.44, D.46, T.48, D.167, S.168 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.44, B:D.46, B:D.167, H2O.15, H2O.22, H2O.23 MG.13: 9 residues within 4Å: Chain A: A.188, S.189, N.190 Chain B: A.188, S.189, N.190 Ligands: CL.3, MG.4, CL.12 No protein-ligand interaction detected (PLIP) MG.19: 5 residues within 4Å: Chain C: D.44, D.46, T.48, D.167, S.168 6 PLIP interactions: 3 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.44, C:D.46, C:D.167, H2O.28, H2O.34, H2O.36 MG.22: 9 residues within 4Å: Chain C: A.188, S.189, N.190 Chain D: A.188, S.189, N.190 Ligands: CL.21, CL.30, MG.31 No protein-ligand interaction detected (PLIP) MG.28: 5 residues within 4Å: Chain D: D.44, D.46, T.48, D.167, S.168 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.44, D:D.46, D:D.167, H2O.40, H2O.47, H2O.48 MG.31: 9 residues within 4Å: Chain C: A.188, S.189, N.190 Chain D: A.188, S.189, N.190 Ligands: CL.21, MG.22, CL.30 No protein-ligand interaction detected (PLIP)

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 5 residues within 4Å: Chain A: D.44, T.112, G.113, K.152, N.170 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.113, A:N.170 Water bridges: A:I.45, A:D.46, A:N.170 Salt bridges: A:K.152 ACT.11: 5 residues within 4Å: Chain B: D.44, T.112, G.113, K.152, N.170 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.113, B:N.170 Water bridges: B:I.45, B:D.46, B:N.170 Salt bridges: B:K.152 ACT.20: 5 residues within 4Å: Chain C: D.44, T.112, G.113, K.152, N.170 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:T.112, C:G.113, C:N.170 Water bridges: C:I.45, C:D.46, C:N.170 Salt bridges: C:K.152 ACT.29: 5 residues within 4Å: Chain D: D.44, T.112, G.113, K.152, N.170 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:T.112, D:G.113, D:N.170 Water bridges: D:I.45, D:D.46, D:N.170 Salt bridges: D:K.152

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 7 residues within 4Å: Chain A: S.189 Chain B: S.189 Chain C: V.12 Chain D: V.12 Ligands: MG.4, CL.12, MG.13 Ligand excluded by PLIP CL.12: 7 residues within 4Å: Chain A: S.189 Chain B: S.189 Chain C: V.12 Chain D: V.12 Ligands: CL.3, MG.4, MG.13 Ligand excluded by PLIP CL.21: 7 residues within 4Å: Chain A: V.12 Chain B: V.12 Chain C: S.189 Chain D: S.189 Ligands: MG.22, CL.30, MG.31 Ligand excluded by PLIP CL.30: 7 residues within 4Å: Chain A: V.12 Chain B: V.12 Chain C: S.189 Chain D: S.189 Ligands: CL.21, MG.22, MG.31 Ligand excluded by PLIP

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

EDO.5: 4 residues within 4Å: Chain A: V.140, I.141, F.142, W.155 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: R.176, A.180, R.181, G.182 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: W.57 Chain B: I.89, P.90, R.95 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: E.78, N.82, T.117, K.118, T.119 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: P.38, M.39, A.40, A.107 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain B: V.140, I.141, F.142, W.155 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain B: R.176, A.180, R.181, G.182 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain A: I.89, P.90, R.95 Chain B: W.57 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain B: E.78, N.82, T.117, K.118, T.119 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain B: P.38, M.39, A.40, A.107 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain C: V.140, I.141, F.142, W.155 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain C: R.176, A.180, R.181, G.182 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain C: W.57 Chain D: I.89, P.90, R.95 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain C: E.78, N.82, T.117, K.118, T.119 Ligand excluded by PLIP EDO.27: 4 residues within 4Å: Chain C: P.38, M.39, A.40, A.107 Ligand excluded by PLIP EDO.32: 4 residues within 4Å: Chain D: V.140, I.141, F.142, W.155 Ligand excluded by PLIP EDO.33: 4 residues within 4Å: Chain D: R.176, A.180, R.181, G.182 Ligand excluded by PLIP EDO.34: 4 residues within 4Å: Chain C: I.89, P.90, R.95 Chain D: W.57 Ligand excluded by PLIP EDO.35: 5 residues within 4Å: Chain D: E.78, N.82, T.117, K.118, T.119 Ligand excluded by PLIP EDO.36: 4 residues within 4Å: Chain D: P.38, M.39, A.40, A.107 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Leone, R. et al., Structural insights into the catalytic mechanism of the bacterial class B phosphatase AphA belonging to the DDDD superfamily of phosphohydrolases. J.Mol.Biol. (2008)

Release Date

2008-11-11

Peptides

Class B acid phosphatase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Class B acid phosphatase

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