SMTL ID : 2qfp.2 (1 other biounit)

Crystal structure of red kidney bean purple acid phosphatase in complex with fluoride

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

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

FE.1: 9 residues within 4Å: Chain A: D.127, D.156, Y.159, H.194, H.315, H.317 Ligands: ZN.2, SO4.3, F.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.127, A:D.156, A:Y.159, A:H.317 FE.14: 9 residues within 4Å: Chain B: D.127, D.156, Y.159, H.194, H.315, H.317 Ligands: ZN.15, SO4.16, F.17 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.127, B:D.156, B:Y.159, B:H.317

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, F.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.156, A:H.278, A:H.315 ZN.15: 7 residues within 4Å: Chain B: D.127, D.156, N.193, H.278, H.315 Ligands: FE.14, F.17 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.156, B:H.278, B:H.315

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

SO4.3: 9 residues within 4Å: Chain A: H.194, H.287, H.317, Y.357 Ligands: FE.1, F.4, NA.10, NA.11, SO4.13 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:H.194, A:H.287, A:H.317 SO4.12: 6 residues within 4Å: Chain A: R.250 Chain B: H.288, E.291 Ligands: SO4.16, NA.22, NA.23 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Salt bridges: A:R.250, B:H.288 Water bridges: B:N.193, B:E.291 SO4.13: 7 residues within 4Å: Chain A: H.287, H.288 Chain B: R.250 Ligands: SO4.3, NA.9, NA.10, NA.11 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Water bridges: A:H.288, B:R.250 Salt bridges: A:H.288, B:R.250 SO4.16: 8 residues within 4Å: Chain B: H.194, H.287, H.317, Y.357 Ligands: SO4.12, FE.14, F.17, NA.23 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.357 Salt bridges: B:H.194, B:H.287, B:H.317

2 x F: FLUORIDE ION(Non-covalent)

F.4: 10 residues within 4Å: Chain A: D.127, D.156, N.193, H.194, H.278, H.315 Ligands: FE.1, ZN.2, SO4.3, NA.10 No protein-ligand interaction detected (PLIP) F.17: 10 residues within 4Å: Chain B: D.127, D.156, N.193, H.194, H.315, H.317 Ligands: FE.14, ZN.15, SO4.16, NA.23 No protein-ligand interaction detected (PLIP)

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

NAG.5: 2 residues within 4Å: Chain A: N.73, N.165 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.73 NAG.6: 7 residues within 4Å: Chain A: M.3, D.8, F.132, N.135, S.139, E.142, R.180 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.139, A:S.139 NAG.7: 4 residues within 4Å: Chain A: K.387, N.388, H.391, W.411 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.388, A:N.388 NAG.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 NAG.18: 2 residues within 4Å: Chain B: N.73, N.165 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.73 NAG.19: 7 residues within 4Å: Chain B: M.3, S.7, 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.20: 4 residues within 4Å: Chain B: K.387, N.388, H.391, W.411 No protein-ligand interaction detected (PLIP) NAG.21: 3 residues within 4Å: Chain B: Y.16, R.100, N.101 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.101

5 x NA: SODIUM ION(Non-functional Binders)

NA.9: 3 residues within 4Å: Chain A: H.287 Ligands: NA.11, SO4.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.287 NA.10: 7 residues within 4Å: Chain A: N.193, H.194, H.288, H.315 Ligands: SO4.3, F.4, SO4.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.193 NA.11: 4 residues within 4Å: Chain A: H.287 Ligands: SO4.3, NA.9, SO4.13 No protein-ligand interaction detected (PLIP) NA.22: 2 residues within 4Å: Chain B: H.287 Ligands: SO4.12 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.287 NA.23: 6 residues within 4Å: Chain B: N.193, H.288, H.315 Ligands: SO4.12, SO4.16, F.17 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.193, B:H.194

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
C

B
D

Purple acid phosphatase

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