SMTL ID : 6ofd.2 (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

2 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.1: 3 residues within 4Å: Chain A: Y.51, R.135, N.136 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG.4: 6 residues within 4Å: Chain B: K.422, N.423, R.424, T.425, H.426, W.446 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.446

1 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.2: 3 residues within 4Å: Chain A: N.108, P.199, N.200 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.199

1 x NAG- NAG- BMA- MAN- MAN- FUC: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN-MAN-FUC.3: 5 residues within 4Å: Chain A: K.422, N.423, T.425, H.426, W.446 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.446

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.51, R.135, N.136 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.51 Hydrogen bonds: B:N.136

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.1 ZN.20: 6 residues within 4Å: Chain B: D.162, D.191, N.228, H.313, H.350 Ligands: FE.21 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.191, B:H.313, B:H.350, H2O.25

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

FE.7: 7 residues within 4Å: Chain A: D.162, D.191, Y.194, H.350, H.352 Ligands: ZN.6, MF1.9 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.1 FE.21: 6 residues within 4Å: Chain B: D.162, D.191, Y.194, H.350, H.352 Ligands: ZN.20 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.25

3 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 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.167 Hydrogen bonds: A:D.43, A:D.43, A:N.170, A:S.174 Water bridges: A:D.43, A:D.43, A:S.174, A:E.177 NAG.22: 7 residues within 4Å: Chain B: M.38, S.42, D.43, V.44, F.167, N.170, S.174 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.167 Hydrogen bonds: B:D.43, B:D.43, B:N.170, B:S.174 NAG.24: 2 residues within 4Å: Chain B: N.108, N.200 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.108, B:N.200

1 x MF1: [(S)-(naphthalen-1-yl)(octadecyloxy)methyl]phosphonic acid(Non-covalent)

MF1.9: 14 residues within 4Å: Chain A: N.33, K.34, R.36, Y.194, R.197, N.228, H.229, H.322, H.323, H.352, Y.392, V.394 Ligands: FE.7, SO4.17 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:R.197, A:Y.392, A:Y.392 Hydrogen bonds: A:Y.392, A:Y.392 Water bridges: A:H.322, A:Y.392 pi-Stacking: A:H.322, A:H.323

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

NA.10: 5 residues within 4Å: Chain A: G.284, R.285, K.333 Chain B: Y.280, E.326 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.285, A:K.333, A:K.333 Water bridges: B:S.314 NA.11: 6 residues within 4Å: Chain A: W.87, S.88, G.92, R.93, R.95 Ligands: SO4.14 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.88, A:S.88, A:R.93, A:R.95 NA.25: 2 residues within 4Å: Chain B: T.332 Ligands: SO4.26 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.332

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

SO4.12: 4 residues within 4Å: Chain A: M.399, Q.401, Q.403, R.410 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.401 Water bridges: A:Q.403 Salt bridges: A:R.410 SO4.13: 3 residues within 4Å: Chain A: K.301, R.302, S.303 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.302, A:S.303 Water bridges: A:V.300, A:S.303, A:S.303 SO4.14: 6 residues within 4Å: Chain A: S.88, N.91, R.95, K.123, Y.128 Ligands: NA.11 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.88, A:N.91 Salt bridges: A:R.95, A:K.123 SO4.15: 1 residues within 4Å: Chain A: R.433 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.433, A:Q.435 Salt bridges: A:R.433 SO4.16: 5 residues within 4Å: Chain A: R.285, Y.290, T.332, K.333 Chain B: E.326 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Y.290, A:Y.290 Water bridges: A:T.332, B:M.325, B:M.325, B:E.326 Salt bridges: A:K.333 SO4.17: 1 residues within 4Å: Ligands: MF1.9 No protein-ligand interaction detected (PLIP) SO4.26: 5 residues within 4Å: Chain A: E.326 Chain B: R.285, Y.290, K.333 Ligands: NA.25 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.290 Water bridges: B:T.332 Salt bridges: B:R.285, B:K.333 SO4.27: 3 residues within 4Å: Chain B: K.301, R.302, S.303 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.302, B:S.303

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

EDO.18: 1 residues within 4Å: Chain A: P.180 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.180 EDO.23: 3 residues within 4Å: Chain B: S.247, Y.248, H.251 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.247, B:H.251

3 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.19: 5 residues within 4Å: Chain A: N.321, H.322, D.396, S.397, N.398 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.397, A:S.397, A:N.398 Water bridges: A:H.322 PGE.29: 4 residues within 4Å: Chain B: H.322, D.396, S.397, N.398 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.396, B:S.397, B:N.398, B:N.398 Water bridges: B:H.322 PGE.30: 2 residues within 4Å: Chain B: K.340, Y.341 3 PLIP interactions: 3 interactions with chain B Water bridges: B:K.340, B:K.340, B:Y.341

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.28: 4 residues within 4Å: Chain B: M.399, Q.401, Q.403, R.410 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.401, B:R.410 Water bridges: B:Q.403

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

CL.31: 4 residues within 4Å: Chain A: E.326 Chain B: G.284, R.285, K.333 Ligand excluded by PLIP

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
A

B
D

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

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