- 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)
- 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)
- 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:6 interactions with chain A, 1 interactions with chain D- Hydrogen bonds: A:R.298, A:T.299, A:I.330, A:Y.332
- Water bridges: A:R.298, A:A.331, D:E.295
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:4 interactions with chain D, 1 interactions with chain A- Hydrogen bonds: D:R.298, D:R.298, D:N.329, A:R.298
- 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:2 interactions with chain D, 1 interactions with chain B- Hydrogen bonds: D:E.45, D:E.45, B:N.167
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)
- 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
AB
BC
CD
D
- 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)
- 2 x NAG- FUC: alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 4 x ZN: ZINC ION(Non-covalent)
- 4 x FE: FE (III) ION(Non-covalent)
- 1 x 0LO: 5-phenylpyridine-3-carboxylic acid(Non-covalent)
- 7 x GOL: GLYCEROL(Non-functional Binders)
- 7 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 11 x SO4: SULFATE ION(Non-functional Binders)
- 13 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 2 x ACT: ACETATE ION(Non-functional Binders)
- 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
AB
BC
CD
D