SMTL ID : 6of5.3 (2 other biounits)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 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.18, R.102, N.103 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG.4: 7 residues within 4Å: Chain B: K.389, N.390, R.391, T.392, H.393, W.413, Y.420 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.413

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.2: 3 residues within 4Å: Chain A: N.75, P.166, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.3: 6 residues within 4Å: Chain A: K.389, N.390, H.393, W.413 Ligands: SO4.13, EDO.17 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.413 NAG-NAG-BMA-FUC.5: 3 residues within 4Å: Chain B: Y.18, R.102, N.103 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.102

2 x ZN: ZINC ION(Non-covalent)

ZN.6: 6 residues within 4Å: Chain A: D.129, D.158, N.195, H.280, H.317 Ligands: FE.7 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.158, A:H.280, A:H.317 ZN.19: 6 residues within 4Å: Chain B: D.129, D.158, N.195, H.280, H.317 Ligands: FE.20 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: 6 residues within 4Å: Chain A: D.129, D.158, Y.161, H.317, H.319 Ligands: ZN.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.129, A:D.158, A:Y.161, A:H.319 FE.20: 6 residues within 4Å: Chain B: D.129, D.158, Y.161, H.317, H.319 Ligands: ZN.19 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.129, B:D.158, B:Y.161, B:H.319

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

NAG.8: 5 residues within 4Å: Chain A: M.5, D.10, F.134, N.137, S.141 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.134 Hydrogen bonds: A:D.10, A:D.10, A:S.141 Water bridges: A:D.10, A:N.137, A:N.137, A:S.141, A:S.141 NAG.21: 2 residues within 4Å: Chain B: N.75, N.167 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.167 NAG.22: 6 residues within 4Å: Chain B: S.9, D.10, F.134, N.137, S.141, R.182 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.134 Hydrogen bonds: B:D.10, B:D.10, B:N.137, B:S.141, B:R.182 Water bridges: B:D.10 NAG.34: 3 residues within 4Å: Chain B: P.202, E.203, N.205 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.205

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

SO4.9: 3 residues within 4Å: Chain A: R.34, K.90, Y.91 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.91 Salt bridges: A:R.34 SO4.10: 9 residues within 4Å: Chain A: G.251, R.252, K.300 Chain B: Y.247, Y.250, S.281, E.293 Ligands: SO4.11, NA.27 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.250, B:S.281, B:E.293, A:R.252 Water bridges: B:S.246, B:A.296 Salt bridges: A:K.300 SO4.11: 5 residues within 4Å: Chain A: R.252, Y.257, K.300 Chain B: E.293 Ligands: SO4.10 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Water bridges: B:F.291, B:E.293 Hydrogen bonds: A:Y.257 Salt bridges: A:K.300 SO4.12: 4 residues within 4Å: Chain A: V.267, K.268, R.269, S.270 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.268, A:R.269, A:S.270 SO4.13: 4 residues within 4Å: Chain A: K.389, W.413 Ligands: NAG-NAG-BMA-FUC.3, NAG-NAG-BMA-FUC.3 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.389 SO4.14: 4 residues within 4Å: Chain A: M.366, Q.368, Q.370, R.377 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.368 Water bridges: A:Q.368, A:Q.370, A:R.377 Salt bridges: A:R.377 SO4.15: 2 residues within 4Å: Chain A: L.118, R.391 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.391 SO4.16: 2 residues within 4Å: Chain A: K.61, R.107 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.61, A:R.107 SO4.23: 5 residues within 4Å: Chain B: S.55, N.58, R.62, K.90, Y.95 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.55, B:N.58, B:Y.95 Salt bridges: B:R.62 SO4.24: 1 residues within 4Å: Chain B: R.400 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.400 SO4.25: 3 residues within 4Å: Chain B: N.2, R.164, Y.165 2 PLIP interactions: 2 interactions with chain B Water bridges: B:N.2 Salt bridges: B:R.164 SO4.26: 6 residues within 4Å: Chain B: K.65, G.66, H.83, T.84, T.85, R.87 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.85 Water bridges: B:R.87, B:R.87 Salt bridges: B:R.87

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

EDO.17: 3 residues within 4Å: Chain A: R.391, W.419 Ligands: NAG-NAG-BMA-FUC.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.391 Water bridges: A:R.391 EDO.18: 3 residues within 4Å: Chain A: R.34, Y.91, Q.115 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.34, A:Y.91, A:Q.115 EDO.29: 2 residues within 4Å: Chain B: K.61, R.107 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.61, B:K.61, B:R.107, B:R.107 EDO.30: 3 residues within 4Å: Chain B: N.288, H.289, N.365 2 PLIP interactions: 2 interactions with chain B Water bridges: B:H.289, B:D.363 EDO.31: 3 residues within 4Å: Chain B: Q.368, Q.370, R.377 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.368, B:Q.368, B:Q.370, B:R.377 Water bridges: B:Q.370 EDO.32: 3 residues within 4Å: Chain A: E.293 Chain B: Y.257, K.300 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Water bridges: A:E.293, A:E.295, B:R.252, B:Y.257 Hydrogen bonds: B:K.300, B:K.300 EDO.33: 1 residues within 4Å: Chain B: K.307 No protein-ligand interaction detected (PLIP)

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

NA.27: 5 residues within 4Å: Chain B: Y.247, S.281, E.293, H.317 Ligands: SO4.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.247, B:S.281 NA.28: 4 residues within 4Å: Chain A: E.293 Chain B: G.251, R.252, K.300 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.252, B:K.300, A:E.293 Water bridges: A:E.293

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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