SMTL ID : 2qfr.1

Crystal structure of red kidney bean purple acid phosphatase with bound sulfate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

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

FE.1: 6 residues within 4Å: Chain A: D.127, D.156, Y.159, H.315, H.317 Ligands: ZN.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.127, A:D.156, A:Y.159, A:H.317, H2O.1 FE.9: 6 residues within 4Å: Chain B: D.127, D.156, Y.159, H.315, H.317 Ligands: ZN.10 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.127, B:D.156, B:Y.159, B:H.317, H2O.8

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 7 residues within 4Å: Chain A: D.127, D.156, N.193, H.278, H.315 Ligands: FE.1, SO4.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.156, A:H.278, A:H.315, H2O.1 ZN.10: 7 residues within 4Å: Chain B: D.127, D.156, N.193, H.278, H.315 Ligands: FE.9, SO4.11 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.156, B:H.278, B:H.315, H2O.8

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 7 residues within 4Å: Chain A: N.193, H.194, H.287, H.288, H.315, H.317 Ligands: ZN.2 7 PLIP interactions: 1 interactions with chain B, 6 interactions with chain A Water bridges: B:R.250 Hydrogen bonds: A:N.193 Salt bridges: A:H.194, A:H.287, A:H.288, A:H.315, A:H.317 SO4.4: 4 residues within 4Å: Chain A: R.250, Y.255, K.259, W.302 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.255 Water bridges: A:R.250, A:R.250, A:Y.255 Salt bridges: A:R.250, A:K.259 SO4.11: 7 residues within 4Å: Chain B: N.193, H.194, H.287, H.288, H.317, Y.357 Ligands: ZN.10 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.193, B:H.315, B:Y.357 Salt bridges: B:H.194, B:H.287, B:H.288, B:H.315, B:H.317 Water bridges: A:R.250 SO4.12: 3 residues within 4Å: Chain B: R.250, Y.255, K.259 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.255, B:Y.255 Salt bridges: B:R.250, B:K.259

2 x NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose(Non-covalent)

NDG.5: 2 residues within 4Å: Chain A: N.73, N.165 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.73 Water bridges: A:N.73 NDG.8: 3 residues within 4Å: Chain A: E.43, R.100, N.101 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.101

6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.6: 7 residues within 4Å: Chain A: M.3, D.8, F.132, N.135, S.139, E.142, R.180 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.132 Hydrogen bonds: A:D.8, A:D.8, A:N.135, A:S.139 NAG.7: 4 residues within 4Å: Chain A: K.387, N.388, T.390, H.391 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.388 Hydrogen bonds: A:T.390 NAG.13: 2 residues within 4Å: Chain B: N.73, N.165 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.73 NAG.14: 6 residues within 4Å: Chain B: M.3, D.8, F.132, N.135, S.139, R.180 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.132 Hydrogen bonds: B:D.8, B:D.8, B:N.135, B:S.139, B:R.180 NAG.15: 4 residues within 4Å: Chain B: N.388, T.390, H.391, W.411 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.390 NAG.16: 4 residues within 4Å: Chain B: Y.16, E.43, R.100, N.101 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.16, B:N.101

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schenk, G. et al., Crystal structures of a purple acid phosphatase, representing different steps of this enzyme's catalytic cycle. Bmc Struct.Biol. (2008)

Release Date

2008-10-14

Peptides

Purple acid phosphatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Purple acid phosphatase

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