SMTL ID : 4dsy.2 (1 other biounit)

Crystal structure of red kidney bean purple acid phosphatase in complex with Maybridge fragment CC24201

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

7 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)(Post Translational Modification)(Non-functional Binders)

NAG-FUC-NAG.1: 6 residues within 4Å: Chain A: N.75, P.166, N.167 Chain C: Y.18, D.44, E.45 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: 5 residues within 4Å: Chain A: K.389, N.390, T.392, 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.5: 4 residues within 4Å: Chain B: K.389, N.390, H.393, W.413 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.413 NAG-FUC-NAG.7: 7 residues within 4Å: Chain C: K.389, N.390, R.391, T.392, H.393, W.413, Y.420 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.413 NAG-FUC-NAG.8: 3 residues within 4Å: Chain D: Y.18, R.102, N.103 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG.9: 6 residues within 4Å: Chain D: K.389, N.390, R.391, T.392, H.393, W.413 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:W.413

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

NAG-FUC.4: 3 residues within 4Å: Chain B: Y.18, R.102, N.103 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.18 Hydrogen bonds: B:N.103 Water bridges: B:Y.18, B:E.45 NAG-FUC.6: 3 residues within 4Å: Chain C: Y.18, R.102, N.103 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.18 Hydrogen bonds: C:N.103

4 x ZN: ZINC ION(Non-covalent)

ZN.10: 7 residues within 4Å: Chain A: D.129, D.158, N.195, H.280, H.317 Ligands: FE.11, 0LO.12 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.158, A:H.280, A:H.317 ZN.23: 6 residues within 4Å: Chain B: D.129, D.158, N.195, H.280, H.317 Ligands: FE.24 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.158, B:H.280, B:H.317 ZN.41: 6 residues within 4Å: Chain C: D.129, D.158, N.195, H.280, H.317 Ligands: FE.42 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.158, C:H.280, C:H.317 ZN.46: 6 residues within 4Å: Chain D: D.129, D.158, N.195, H.280, H.317 Ligands: FE.47 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.158, D:H.280, D:H.317

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

FE.11: 6 residues within 4Å: Chain A: D.129, D.158, Y.161, H.319 Ligands: ZN.10, 0LO.12 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.129, A:D.158, A:Y.161, A:H.319 FE.24: 6 residues within 4Å: Chain B: D.129, D.158, Y.161, H.317, H.319 Ligands: ZN.23 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.129, B:D.158, B:Y.161, B:H.319 FE.42: 6 residues within 4Å: Chain C: D.129, D.158, Y.161, H.317, H.319 Ligands: ZN.41 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.129, C:D.158, C:Y.161, C:H.319 FE.47: 6 residues within 4Å: Chain D: D.129, D.158, Y.161, H.317, H.319 Ligands: ZN.46 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.129, D:D.158, D:Y.161, D:H.319

1 x 0LO: 5-phenylpyridine-3-carboxylic acid(Non-covalent)

0LO.12: 12 residues within 4Å: Chain A: D.129, D.158, N.195, H.196, H.289, H.290, H.317, H.319, Y.359 Chain D: R.252 Ligands: ZN.10, FE.11 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

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 8 residues within 4Å: Chain A: R.298, T.299, N.329, I.330, A.331, Y.332 Chain D: M.292, E.295 7 PLIP interactions: 1 interactions with chain D, 6 interactions with chain A Water bridges: D:E.295, A:R.298, A:A.331 Hydrogen bonds: A:R.298, A:T.299, A:I.330, A:Y.332 GOL.27: 5 residues within 4Å: Chain B: V.267, K.268, R.269, S.270, H.418 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.267, B:R.269, B:S.270, B:S.270 GOL.43: 6 residues within 4Å: Chain C: S.55, N.58, R.60, R.62, K.90, Y.95 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.58, C:R.60, C:R.62, C:R.62, C:Y.95, C:Y.95 Water bridges: C:S.55 GOL.48: 4 residues within 4Å: Chain D: M.366, Q.368, Q.370, R.377 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.368, D:Q.370, D:R.377 Water bridges: D:Q.370, D:R.377 GOL.51: 5 residues within 4Å: Chain A: R.298, Y.332 Chain D: R.298, N.329, Y.332 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain D Hydrogen bonds: A:R.298, D:R.298, D:R.298, D:N.329 Water bridges: D:Y.332 GOL.52: 5 residues within 4Å: Chain D: V.267, K.268, R.269, S.270, H.418 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.269, D:S.270 Water bridges: D:V.267 GOL.53: 3 residues within 4Å: Chain D: K.307, Y.308, K.309 5 PLIP interactions: 5 interactions with chain D Water bridges: D:K.307, D:Y.308, D:Y.308, D:K.309, D:K.309

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

NAG.14: 7 residues within 4Å: Chain A: M.5, D.10, V.11, F.134, N.137, S.141, R.182 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.134 Hydrogen bonds: A:D.10, A:D.10, A:N.137, A:S.141, A:R.182 Water bridges: A:S.141, A:E.144 NAG.25: 5 residues within 4Å: Chain B: N.75, N.167 Chain D: Y.18, D.44, E.45 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:N.167, D:E.45, D:E.45 NAG.26: 5 residues within 4Å: Chain B: M.5, D.10, F.134, N.137, S.141 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.134 Hydrogen bonds: B:D.10, B:D.10, B:S.141 NAG.39: 8 residues within 4Å: Chain C: M.5, S.9, D.10, V.11, F.134, N.137, S.141, R.182 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.134 Hydrogen bonds: C:D.10, C:D.10, C:N.137, C:S.141, C:R.182 NAG.40: 5 residues within 4Å: Chain A: Y.18, D.44, E.45 Chain C: N.75, N.167 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:N.167, A:Y.18 Water bridges: A:Y.18, A:E.45 NAG.49: 7 residues within 4Å: Chain D: M.5, S.9, D.10, V.11, F.134, N.137, S.141 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:F.134 Hydrogen bonds: D:D.10, D:D.10, D:N.137, D:S.141 NAG.50: 4 residues within 4Å: Chain B: Y.18, D.44 Chain D: N.75, N.167 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:Y.18, D:N.75, D:N.167 Water bridges: B:Y.18, B:E.45

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

SO4.15: 4 residues within 4Å: Chain A: S.55, N.58, R.62, Y.95 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.55, A:N.58, A:Y.95 Water bridges: A:G.59 Salt bridges: A:R.62 SO4.16: 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:R.269, A:S.270 Salt bridges: A:H.418 SO4.17: 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:R.377 Salt bridges: A:R.377 SO4.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.28: 2 residues within 4Å: Chain B: V.342, K.343 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.343 Water bridges: B:P.341 Salt bridges: B:K.343 SO4.29: 4 residues within 4Å: Chain B: V.32, R.34, Y.91, Q.115 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.115 Water bridges: B:V.32, B:Y.91 SO4.30: 2 residues within 4Å: Chain B: K.90, Y.91 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.91 Salt bridges: B:K.90 SO4.31: 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 Water bridges: B:Q.370, B:R.377 Salt bridges: B:R.377 SO4.38: 2 residues within 4Å: Chain C: N.2, R.3 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.2 Salt bridges: C:R.3 SO4.44: 4 residues within 4Å: Chain C: M.366, Q.368, Q.370, R.377 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Q.368, C:Q.370 Water bridges: C:Q.370, C:R.377, C:R.377 Salt bridges: C:R.377 SO4.54: 4 residues within 4Å: Chain A: E.293 Chain D: R.252, Y.257, K.300 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Y.257, D:Y.257 Water bridges: D:R.252 Salt bridges: D:K.300

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

EDO.19: 2 residues within 4Å: Chain A: P.147, K.148 No protein-ligand interaction detected (PLIP) EDO.20: 2 residues within 4Å: Chain A: V.342, K.343 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.343 EDO.21: 4 residues within 4Å: Chain A: I.362, D.363, S.364, N.365 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.364, A:N.365, A:N.365 Water bridges: A:H.289 EDO.32: 2 residues within 4Å: Chain B: K.61, R.107 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.61, B:R.107, B:R.107 EDO.33: 4 residues within 4Å: Chain B: N.288, H.289, D.363, N.365 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.288, B:D.363, B:S.364, B:N.365 Water bridges: B:H.289 EDO.34: 2 residues within 4Å: Chain B: K.1, R.3 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.1, B:K.1, B:R.3 EDO.35: 1 residues within 4Å: Chain B: R.3 No protein-ligand interaction detected (PLIP) EDO.36: 4 residues within 4Å: Chain B: P.166, N.167, H.168, E.203 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.167, B:E.203 EDO.37: 2 residues within 4Å: Chain C: K.61, R.107 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.61, C:R.107, C:R.107 EDO.45: 3 residues within 4Å: Chain C: D.163, N.195, H.196 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:N.195, C:H.196 Water bridges: C:D.163, B:G.253 EDO.55: 5 residues within 4Å: Chain D: N.288, H.289, D.363, S.364, N.365 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.363, D:S.364, D:N.365, D:N.365 Water bridges: D:N.288 EDO.56: 2 residues within 4Å: Chain D: S.48, R.102 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.48 Water bridges: D:S.49 EDO.57: 4 residues within 4Å: Chain A: G.253 Chain D: D.163, N.195, H.196 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain D Water bridges: A:R.252, A:G.253, D:D.163 Hydrogen bonds: D:N.195, D:H.196

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.22: 1 residues within 4Å: Chain A: R.391 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.391 ACT.58: 2 residues within 4Å: Chain D: K.61, R.107 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:K.61, D:R.107

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

2012-09-19

Peptides

Purple acid phosphatase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Purple acid phosphatase

Related Entries With Identical Sequence