SMTL ID : 4dhl.1 (1 other biounit)

Crystal structure of red kidney bean purple acid phosphatase in complex with Maybridge fragment MO07123

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

4 x NAG- FUC- NAG: alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Non-functional Binders)

NAG-FUC-NAG.1: 3 residues within 4Å: Chain A: N.75, P.166, N.167 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.166 NAG-FUC-NAG.2: 3 residues within 4Å: Chain A: Y.18, R.102, N.103 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG.3: 4 residues within 4Å: Chain A: K.389, N.390, H.393, W.413 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.393 Hydrophobic interactions: A:W.413 NAG-FUC-NAG.4: 6 residues within 4Å: Chain B: K.389, N.390, R.391, T.392, H.393, W.413 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.413

1 x NAG- FUC: alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.5: 3 residues within 4Å: Chain B: Y.18, R.102, N.103 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.18 Hydrogen bonds: B:N.103

2 x ZN: ZINC ION(Non-covalent)

ZN.6: 7 residues within 4Å: Chain A: D.129, D.158, N.195, H.280, H.317 Ligands: FE.7, 0K7.8 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.158, A:H.280, A:H.317 ZN.14: 7 residues within 4Å: Chain B: D.129, D.158, N.195, H.280, H.317 Ligands: FE.15, 0K7.16 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.158, B:H.280, B:H.317

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

FE.7: 7 residues within 4Å: Chain A: D.129, D.158, Y.161, H.317, H.319 Ligands: ZN.6, 0K7.8 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.129, A:D.158, A:Y.161, A:H.319 FE.15: 7 residues within 4Å: Chain B: D.129, D.158, Y.161, H.317, H.319 Ligands: ZN.14, 0K7.16 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.129, B:D.158, B:Y.161, B:H.319

2 x 0K7: 2-(4-methylphenyl)-1,3-thiazole-4-carboxylic acid(Non-covalent)

0K7.8: 12 residues within 4Å: Chain A: D.158, Y.161, N.195, H.196, H.289, H.290, H.317, H.319, Y.359 Chain B: R.252 Ligands: ZN.6, FE.7 5 PLIP interactions: 5 interactions with chain A Salt bridges: A:H.196, A:H.290, A:H.317, A:H.319 pi-Stacking: A:H.289 0K7.16: 11 residues within 4Å: Chain B: D.129, D.158, N.195, H.196, H.289, H.290, H.317, H.319, Y.359 Ligands: ZN.14, FE.15 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.195 Salt bridges: B:H.196, B:H.290, B:H.317, B:H.319 Water bridges: A:R.252, A:R.252

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 8 residues within 4Å: Chain A: R.298, T.299, N.329, I.330, A.331, Y.332 Chain B: M.292, E.295 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.298, A:T.299, A:I.330, A:Y.332 Water bridges: A:R.298, B:E.295 GOL.17: 2 residues within 4Å: Chain B: K.307, Y.308 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.307, B:K.309

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

SO4.10: 5 residues within 4Å: Chain A: S.55, N.58, R.62, K.90, Y.95 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.55, A:N.58, A:Y.95 Water bridges: A:S.55 Salt bridges: A:R.62, A:K.90 SO4.11: 4 residues within 4Å: Chain A: K.268, R.269, S.270, H.418 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.269, A:S.270 Salt bridges: A:K.268, A:H.418 SO4.18: 3 residues within 4Å: Chain B: K.268, R.269, S.270 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.269, B:S.270 Salt bridges: B:K.268

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

EDO.12: 2 residues within 4Å: Chain A: P.147, K.148 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.147 EDO.19: 7 residues within 4Å: Chain A: M.292 Chain B: T.299, N.329, I.330, A.331, Y.332 Ligands: EDO.21 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.299, B:N.329, B:Y.332 EDO.20: 4 residues within 4Å: Chain A: G.253 Chain B: D.163, N.195, H.196 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:G.253, B:D.163 Hydrogen bonds: B:D.163 EDO.21: 5 residues within 4Å: Chain A: Y.332 Chain B: R.298, N.329, Y.332 Ligands: EDO.19 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.298, B:R.298, B:N.329 Water bridges: B:E.295, B:E.295 EDO.23: 5 residues within 4Å: Chain B: Y.165, P.166, N.167, H.168, E.203 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.167, B:H.168, B:E.203 EDO.24: 3 residues within 4Å: Chain B: S.214, Y.215, H.218 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.218

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

NAG.13: 6 residues within 4Å: Chain A: M.5, D.10, V.11, F.134, N.137, S.141 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.134 Hydrogen bonds: A:D.10, A:D.10, A:N.137, A:S.141 Water bridges: A:S.141, A:E.144 NAG.22: 7 residues within 4Å: Chain B: M.5, S.9, D.10, V.11, F.134, N.137, S.141 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.134 Hydrogen bonds: B:D.10, B:D.10, B:N.137, B:S.141 Water bridges: B:S.141 NAG.25: 2 residues within 4Å: Chain B: N.75, N.167 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.167

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Feder, D. et al., Identification of purple acid phosphatase inhibitors by fragment-based screening: promising new leads for osteoporosis therapeutics. Chem.Biol.Drug Des. (2012)

Release Date

2012-12-12

Peptides

Purple acid phosphatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Purple acid phosphatase

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