SMTL ID : 6of5.2 (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

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: 6 residues within 4Å: Chain B: K.389, N.390, R.391, T.392, H.393, W.413 No protein-ligand interaction detected (PLIP)

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.75, P.166, N.167 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.166

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.389, N.390, T.392, H.393, W.413 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A: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, MFJ.20 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.158, A:H.280, A:H.317 ZN.21: 6 residues within 4Å: Chain B: D.129, D.158, N.195, H.280, H.317 Ligands: FE.22 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.319 Ligands: ZN.6, MFJ.20 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.129, A:D.158, A:Y.161, A:H.319 FE.22: 6 residues within 4Å: Chain B: D.129, D.158, Y.161, H.317, H.319 Ligands: ZN.21 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.129, B:D.158, B:Y.161, B:H.319

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

NAG.8: 6 residues within 4Å: Chain A: M.5, D.10, V.11, F.134, N.137, S.141 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.10, A:D.10, A:N.137, A:S.141, A:R.182 Water bridges: A:E.144 NAG.23: 7 residues within 4Å: Chain B: M.5, S.9, D.10, V.11, F.134, N.137, S.141 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.10, B:D.10, B:N.137, B:S.141 NAG.25: 2 residues within 4Å: Chain B: N.75, N.167 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.75, B:N.167

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

SO4.9: 3 residues within 4Å: Chain A: Q.368, Q.370, R.377 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.368, A:Q.370 Water bridges: A:Q.370, A:Q.370 Salt bridges: A:R.377 SO4.10: 3 residues within 4Å: Chain A: K.268, R.269, S.270 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.269, A:S.270 Water bridges: A:V.267 Salt bridges: A:K.268, A:H.418 SO4.11: 5 residues within 4Å: Chain A: S.55, N.58, R.62, Y.95 Ligands: NA.14 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.55, A:N.58 Salt bridges: A:R.62 SO4.12: 1 residues within 4Å: Chain A: R.400 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.400 SO4.26: 4 residues within 4Å: Chain A: E.293 Chain B: R.252, Y.257, K.300 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain B Water bridges: A:M.292, A:E.293, B:R.252, B:R.252 Hydrogen bonds: B:Y.257, B:Y.257 Salt bridges: B:R.252, B:K.300 SO4.27: 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, B:S.270 SO4.28: 3 residues within 4Å: Chain B: R.34, Y.91, Q.115 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.91, B:Q.115 Salt bridges: B:R.34

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

NA.13: 4 residues within 4Å: Chain A: G.251, R.252, K.300 Chain B: E.293 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.252, A:K.300, B:E.293 Water bridges: B:S.281 NA.14: 6 residues within 4Å: Chain A: W.54, S.55, G.59, R.60, R.62 Ligands: SO4.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.55, A:S.55, A:R.60 NA.29: 4 residues within 4Å: Chain A: E.293 Chain B: G.251, R.252, K.300 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Water bridges: A:E.293 Hydrogen bonds: B:R.252, B:K.300, B:K.300

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

EDO.15: 1 residues within 4Å: Chain A: P.147 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.147 EDO.16: 6 residues within 4Å: Chain A: T.299, N.329, I.330, Y.332 Chain B: M.292, E.295 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.299, A:N.329, A:Y.332 Water bridges: B:E.295 EDO.17: 4 residues within 4Å: Chain A: Y.359 Ligands: PGE.19, MFJ.20, PGE.36 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.359, A:Y.359 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:S.214 EDO.30: 3 residues within 4Å: Chain B: G.253 Ligands: MFJ.20, PGE.36 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Water bridges: A:N.195, B:R.252, B:G.253, B:G.253 EDO.31: 6 residues within 4Å: Chain B: D.163, Y.165, P.166, N.167, H.168, E.203 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.165, B:N.167, B:H.168 EDO.32: 6 residues within 4Å: Chain A: M.292 Chain B: T.299, N.329, I.330, A.331, Y.332 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.330, B:Y.332 Water bridges: B:R.298

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

PGE.18: 7 residues within 4Å: Chain A: N.288, H.289, I.362, D.363, S.364, N.365 Ligands: PGE.36 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.364, A:S.364, A:N.365 Water bridges: A:H.289 PGE.19: 5 residues within 4Å: Chain A: R.164, Y.359 Ligands: EDO.17, MFJ.20, PGE.36 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.359 PGE.34: 5 residues within 4Å: Chain B: H.289, I.362, D.363, S.364, N.365 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.364, B:N.365, B:N.365 Water bridges: B:H.289 PGE.35: 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 PGE.36: 6 residues within 4Å: Chain B: R.252 Ligands: EDO.17, PGE.18, PGE.19, MFJ.20, EDO.30 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.252

1 x MFJ: [(R)-{[(2E,4Z,8Z)-dodeca-2,4,8-trien-1-yl]oxy}(naphthalen-1-yl)methyl]phosphonic acid(Non-covalent)

MFJ.20: 19 residues within 4Å: Chain A: D.129, D.158, Y.161, R.164, N.195, H.196, H.289, H.290, E.293, H.317, H.319, Y.359 Chain B: R.252 Ligands: ZN.6, FE.7, EDO.17, PGE.19, EDO.30, PGE.36 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:R.164, B:R.252 Hydrogen bonds: A:H.290 pi-Stacking: A:H.289, A:H.290

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.33: 4 residues within 4Å: Chain B: M.366, Q.368, Q.370, R.377 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.368, B:R.377 Water bridges: B:Q.370, B:R.377

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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