SMTL ID : 6ofd.3 (2 other biounits)

The crystal structure of octadecyloxy(naphthalen-1-yl)methylphosphonic acid in complex with red kidney bean purple acid phosphatase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

3 x NAG- NAG- BMA- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-FUC.1: 3 residues within 4Å: Chain A: Y.51, R.135, N.136 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.3: 7 residues within 4Å: Chain A: K.422, N.423, T.425, H.426, W.446 Ligands: SO4.13, EDO.17 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.446 NAG-NAG-BMA-FUC.5: 3 residues within 4Å: Chain B: Y.51, R.135, N.136 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.135

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.2: 3 residues within 4Å: Chain A: N.108, P.199, N.200 No protein-ligand interaction detected (PLIP)

1 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

NAG-FUC-NAG.4: 7 residues within 4Å: Chain B: K.422, N.423, R.424, T.425, H.426, W.446, Y.453 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.446

2 x ZN: ZINC ION(Non-covalent)

ZN.6: 6 residues within 4Å: Chain A: D.162, D.191, N.228, H.313, H.350 Ligands: FE.7 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.191, A:H.313, A:H.350, H2O.10 ZN.18: 6 residues within 4Å: Chain B: D.162, D.191, N.228, H.313, H.350 Ligands: FE.19 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.191, B:H.313, B:H.350, H2O.18

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

FE.7: 7 residues within 4Å: Chain A: D.162, D.191, Y.194, H.229, H.350, H.352 Ligands: ZN.6 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.162, A:D.191, A:Y.194, A:H.352, H2O.10 FE.19: 6 residues within 4Å: Chain B: D.162, D.191, Y.194, H.350, H.352 Ligands: ZN.18 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.162, B:D.191, B:Y.194, B:H.352, H2O.18

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

NAG.8: 6 residues within 4Å: Chain A: M.38, D.43, V.44, F.167, N.170, S.174 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.167 Hydrogen bonds: A:D.43, A:D.43, A:S.174 Water bridges: A:D.43, A:D.43, A:S.174 NAG.20: 1 residues within 4Å: Chain B: N.108 No protein-ligand interaction detected (PLIP) NAG.21: 7 residues within 4Å: Chain B: M.38, S.42, D.43, V.44, F.167, N.170, S.174 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.167 Hydrogen bonds: B:D.43, B:D.43, B:N.170, B:S.174 Water bridges: B:D.43 NAG.31: 2 residues within 4Å: Chain B: P.235, N.238 No protein-ligand interaction detected (PLIP)

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

SO4.9: 3 residues within 4Å: Chain A: R.67, K.123, Y.124 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.124 Salt bridges: A:R.67 SO4.10: 9 residues within 4Å: Chain A: G.284, R.285, K.333 Chain B: Y.280, Y.283, S.314, E.326 Ligands: SO4.11, NA.22 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.283, B:S.314, B:E.326, A:R.285 Water bridges: B:S.279, B:A.329 Salt bridges: A:K.333 SO4.11: 5 residues within 4Å: Chain A: R.285, Y.290, K.333 Chain B: E.326 Ligands: SO4.10 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.290 Water bridges: A:K.333, B:M.325 Salt bridges: A:K.333 SO4.12: 4 residues within 4Å: Chain A: V.300, K.301, R.302, S.303 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.302, A:S.303 Salt bridges: A:K.301 SO4.13: 4 residues within 4Å: Chain A: K.422, W.446 Ligands: NAG-NAG-BMA-FUC.3, NAG-NAG-BMA-FUC.3 No protein-ligand interaction detected (PLIP) SO4.14: 4 residues within 4Å: Chain A: M.399, Q.401, Q.403, R.410 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.401 Water bridges: A:Q.403, A:R.410 Salt bridges: A:R.410 SO4.15: 2 residues within 4Å: Chain A: L.151, R.424 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.424 SO4.16: 2 residues within 4Å: Chain A: K.94, R.140 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.94, A:R.140 SO4.24: 4 residues within 4Å: Chain B: S.88, N.91, R.95, K.123 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.88, B:N.91 Water bridges: B:S.88, B:R.93 Salt bridges: B:R.95 SO4.25: 1 residues within 4Å: Chain B: R.433 5 PLIP interactions: 5 interactions with chain B Water bridges: B:E.411, B:R.433, B:R.433, B:R.433 Salt bridges: B:R.433 SO4.26: 4 residues within 4Å: Chain B: N.35, R.197, Y.198, P.199 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.35, B:R.197 Water bridges: B:N.35, B:R.197, B:R.197

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

EDO.17: 4 residues within 4Å: Chain A: R.424, T.425, W.452 Ligands: NAG-NAG-BMA-FUC.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.424 Water bridges: A:R.424, A:R.424 EDO.27: 2 residues within 4Å: Chain B: K.94, R.140 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.94, B:K.94, B:R.140, B:R.140 EDO.28: 3 residues within 4Å: Chain B: N.321, H.322, N.398 2 PLIP interactions: 2 interactions with chain B Water bridges: B:H.322, B:D.396 EDO.29: 3 residues within 4Å: Chain B: Q.401, Q.403, R.410 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.401, B:Q.403, B:R.410 Water bridges: B:R.410 EDO.30: 3 residues within 4Å: Chain A: E.326 Chain B: Y.290, K.333 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.333 Water bridges: B:R.285, A:F.324

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

NA.22: 5 residues within 4Å: Chain B: Y.280, S.314, E.326, H.350 Ligands: SO4.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.314, B:H.350 NA.23: 4 residues within 4Å: Chain A: E.326 Chain B: G.284, R.285, K.333 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.285, B:K.333, B:K.333 Water bridges: A:E.326, A:A.329

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Feder, D. et al., Synthesis, evaluation and structural investigations of potent purple acid phosphatase inhibitors as drug leads for osteoporosis. Eur.J.Med.Chem. (2019)

Release Date

2019-09-04

Peptides

Fe(3+)-Zn(2+) purple acid phosphatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

Fe(3+)-Zn(2+) purple acid phosphatase

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