- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.30 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 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
- 4 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: 5 residues within 4Å:- Chain A: N.75, P.166, N.167
- Chain D: Y.18, D.44
1 PLIP interactions:1 interactions with chain A- Hydrophobic interactions: A:P.166
NAG-NAG-BMA-FUC.5: 5 residues within 4Å:- Chain B: N.75, P.166, N.167
- Chain C: Y.18, D.44
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA-FUC.6: 6 residues within 4Å:- Chain B: K.389, N.390, H.393, W.413
- Ligands: SO4.33, EDO.37
1 PLIP interactions:1 interactions with chain B- Hydrophobic interactions: B:W.413
NAG-NAG-BMA-FUC.10: 3 residues within 4Å:- Chain D: Y.18, R.102, N.103
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:R.102
- 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
- 1 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)
ZN.11: 7 residues within 4Å:- Chain A: D.129, D.158, N.195, H.280, H.317
- Ligands: FE.12, MFJ.25
3 PLIP interactions:3 interactions with chain A- Metal complexes: A:D.158, A:H.280, A:H.317
ZN.26: 6 residues within 4Å:- Chain B: D.129, D.158, N.195, H.280, H.317
- Ligands: FE.27
3 PLIP interactions:3 interactions with chain B- Metal complexes: B:D.158, B:H.280, B:H.317
ZN.39: 6 residues within 4Å:- Chain C: D.129, D.158, N.195, H.280, H.317
- Ligands: FE.40
3 PLIP interactions:3 interactions with chain C- Metal complexes: C:D.158, C:H.280, C:H.317
ZN.55: 6 residues within 4Å:- Chain D: D.129, D.158, N.195, H.280, H.317
- Ligands: FE.56
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.12: 6 residues within 4Å:- Chain A: D.129, D.158, Y.161, H.319
- Ligands: ZN.11, MFJ.25
4 PLIP interactions:4 interactions with chain A- Metal complexes: A:D.129, A:D.158, A:Y.161, A:H.319
FE.27: 6 residues within 4Å:- Chain B: D.129, D.158, Y.161, H.317, H.319
- Ligands: ZN.26
4 PLIP interactions:4 interactions with chain B- Metal complexes: B:D.129, B:D.158, B:Y.161, B:H.319
FE.40: 6 residues within 4Å:- Chain C: D.129, D.158, Y.161, H.317, H.319
- Ligands: ZN.39
4 PLIP interactions:4 interactions with chain C- Metal complexes: C:D.129, C:D.158, C:Y.161, C:H.319
FE.56: 6 residues within 4Å:- Chain D: D.129, D.158, Y.161, H.317, H.319
- Ligands: ZN.55
4 PLIP interactions:4 interactions with chain D- Metal complexes: D:D.129, D:D.158, D:Y.161, D:H.319
- 7 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
NAG.13: 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.28: 5 residues within 4Å:- Chain B: M.5, D.10, F.134, N.137, S.141
9 PLIP interactions:9 interactions with chain B- Hydrophobic interactions: B:F.134
- Hydrogen bonds: B:D.10, B:D.10, B:S.141
- Water bridges: B:D.10, B:N.137, B:N.137, B:S.141, B:S.141
NAG.41: 7 residues within 4Å:- Chain C: M.5, S.9, D.10, V.11, F.134, N.137, S.141
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:D.10, C:D.10, C:N.137, C:S.141
NAG.43: 4 residues within 4Å:- Chain B: Y.18, D.44
- Chain C: N.75, N.167
3 PLIP interactions:2 interactions with chain C, 1 interactions with chain B- Hydrogen bonds: C:N.75, C:N.167, B:Y.18
NAG.57: 4 residues within 4Å:- Chain A: Y.18, D.44
- Chain D: N.75, N.167
2 PLIP interactions:1 interactions with chain A, 1 interactions with chain D- Hydrogen bonds: A:Y.18, D:N.167
NAG.58: 6 residues within 4Å:- Chain D: S.9, D.10, F.134, N.137, S.141, R.182
7 PLIP interactions:7 interactions with chain D- Hydrophobic interactions: D:F.134
- Hydrogen bonds: D:D.10, D:D.10, D:N.137, D:S.141, D:R.182
- Water bridges: D:D.10
NAG.70: 3 residues within 4Å:- Chain D: P.202, E.203, N.205
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:N.205
- 19 x SO4: SULFATE ION(Non-functional Binders)
SO4.14: 3 residues within 4Å:- Chain A: Q.368, Q.370, R.377
Ligand excluded by PLIPSO4.15: 3 residues within 4Å:- Chain A: K.268, R.269, S.270
Ligand excluded by PLIPSO4.16: 5 residues within 4Å:- Chain A: S.55, N.58, R.62, Y.95
- Ligands: NA.19
Ligand excluded by PLIPSO4.17: 1 residues within 4Å:- Chain A: R.400
Ligand excluded by PLIPSO4.29: 3 residues within 4Å:- Chain B: R.34, K.90, Y.91
Ligand excluded by PLIPSO4.30: 9 residues within 4Å:- Chain B: G.251, R.252, K.300
- Chain D: Y.247, Y.250, S.281, E.293
- Ligands: SO4.31, NA.63
Ligand excluded by PLIPSO4.31: 5 residues within 4Å:- Chain B: R.252, Y.257, K.300
- Chain D: E.293
- Ligands: SO4.30
Ligand excluded by PLIPSO4.32: 4 residues within 4Å:- Chain B: V.267, K.268, R.269, S.270
Ligand excluded by PLIPSO4.33: 4 residues within 4Å:- Chain B: K.389, W.413
- Ligands: NAG-NAG-BMA-FUC.6, NAG-NAG-BMA-FUC.6
Ligand excluded by PLIPSO4.34: 4 residues within 4Å:- Chain B: M.366, Q.368, Q.370, R.377
Ligand excluded by PLIPSO4.35: 2 residues within 4Å:- Chain B: L.118, R.391
Ligand excluded by PLIPSO4.36: 2 residues within 4Å:- Chain B: K.61, R.107
Ligand excluded by PLIPSO4.44: 4 residues within 4Å:- Chain A: E.293
- Chain C: R.252, Y.257, K.300
Ligand excluded by PLIPSO4.45: 3 residues within 4Å:- Chain C: K.268, R.269, S.270
Ligand excluded by PLIPSO4.46: 3 residues within 4Å:- Chain C: R.34, Y.91, Q.115
Ligand excluded by PLIPSO4.59: 5 residues within 4Å:- Chain D: S.55, N.58, R.62, K.90, Y.95
Ligand excluded by PLIPSO4.60: 1 residues within 4Å:- Chain D: R.400
Ligand excluded by PLIPSO4.61: 3 residues within 4Å:- Chain D: N.2, R.164, Y.165
Ligand excluded by PLIPSO4.62: 6 residues within 4Å:- Chain D: K.65, G.66, H.83, T.84, T.85, R.87
Ligand excluded by PLIP- 5 x NA: SODIUM ION(Non-functional Binders)
NA.18: 4 residues within 4Å:- Chain A: G.251, R.252, K.300
- Chain C: E.293
4 PLIP interactions:3 interactions with chain A, 1 interactions with chain C- Hydrogen bonds: A:R.252, A:K.300, A:K.300
- Water bridges: C:S.281
NA.19: 6 residues within 4Å:- Chain A: W.54, S.55, G.59, R.60, R.62
- Ligands: SO4.16
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:S.55, A:S.55, A:R.60
NA.47: 4 residues within 4Å:- Chain A: E.293
- Chain C: G.251, R.252, K.300
4 PLIP interactions:2 interactions with chain A, 2 interactions with chain C- Water bridges: A:Y.247, A:E.293
- Hydrogen bonds: C:R.252, C:K.300
NA.63: 5 residues within 4Å:- Chain D: Y.247, S.281, E.293, H.317
- Ligands: SO4.30
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:S.281, D:E.293
NA.64: 4 residues within 4Å:- Chain B: E.293
- Chain D: G.251, R.252, K.300
4 PLIP interactions:2 interactions with chain D, 2 interactions with chain B- Hydrogen bonds: D:R.252, D:K.300, B:E.293
- Water bridges: B:E.293
- 14 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.20: 1 residues within 4Å:- Chain A: P.147
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:P.147
EDO.21: 6 residues within 4Å:- Chain A: T.299, N.329, I.330, Y.332
- Chain C: M.292, E.295
4 PLIP interactions:1 interactions with chain C, 3 interactions with chain A- Water bridges: C:E.295
- Hydrogen bonds: A:T.299, A:N.329, A:Y.332
EDO.22: 4 residues within 4Å:- Chain A: Y.359
- Ligands: PGE.24, MFJ.25, PGE.54
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:Y.359, A:Y.359
EDO.37: 3 residues within 4Å:- Chain B: R.391, W.419
- Ligands: NAG-NAG-BMA-FUC.6
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:R.391
- Water bridges: B:R.391
EDO.38: 3 residues within 4Å:- Chain B: R.34, Y.91, Q.115
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:R.34, B:Y.91, B:Q.115
EDO.42: 3 residues within 4Å:- Chain C: S.214, Y.215, H.218
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:S.214
EDO.48: 3 residues within 4Å:- Chain C: G.253
- Ligands: MFJ.25, PGE.54
4 PLIP interactions:3 interactions with chain C, 1 interactions with chain A- Water bridges: C:R.252, C:G.253, C:G.253, A:N.195
EDO.49: 6 residues within 4Å:- Chain C: D.163, Y.165, P.166, N.167, H.168, E.203
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:Y.165, C:N.167, C:H.168
EDO.50: 6 residues within 4Å:- Chain A: M.292
- Chain C: T.299, N.329, I.330, A.331, Y.332
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:I.330, C:Y.332
- Water bridges: C:R.298
EDO.65: 2 residues within 4Å:- Chain D: K.61, R.107
4 PLIP interactions:4 interactions with chain D- Hydrogen bonds: D:K.61, D:K.61, D:R.107, D:R.107
EDO.66: 3 residues within 4Å:- Chain D: N.288, H.289, N.365
2 PLIP interactions:2 interactions with chain D- Water bridges: D:H.289, D:D.363
EDO.67: 3 residues within 4Å:- Chain D: Q.368, Q.370, R.377
5 PLIP interactions:5 interactions with chain D- Hydrogen bonds: D:Q.368, D:Q.368, D:Q.370, D:R.377
- Water bridges: D:Q.370
EDO.68: 3 residues within 4Å:- Chain B: E.293
- Chain D: Y.257, K.300
6 PLIP interactions:4 interactions with chain D, 2 interactions with chain B- Hydrogen bonds: D:K.300, D:K.300
- Water bridges: D:R.252, D:Y.257, B:E.293, B:E.295
EDO.69: 1 residues within 4Å:- Chain D: K.307
No protein-ligand interaction detected (PLIP)- 5 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)
PGE.23: 7 residues within 4Å:- Chain A: N.288, H.289, I.362, D.363, S.364, N.365
- Ligands: PGE.54
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.24: 5 residues within 4Å:- Chain A: R.164, Y.359
- Ligands: EDO.22, MFJ.25, PGE.54
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:Y.359
PGE.52: 5 residues within 4Å:- Chain C: H.289, I.362, D.363, S.364, N.365
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:S.364, C:N.365, C:N.365
- Water bridges: C:H.289
PGE.53: 2 residues within 4Å:- Chain C: K.307, Y.308
2 PLIP interactions:2 interactions with chain C- Water bridges: C:K.307, C:K.309
PGE.54: 6 residues within 4Å:- Chain C: R.252
- Ligands: EDO.22, PGE.23, PGE.24, MFJ.25, EDO.48
1 PLIP interactions:1 interactions with chain C- Water bridges: C: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.25: 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 C: R.252
- Ligands: ZN.11, FE.12, EDO.22, PGE.24, EDO.48, PGE.54
5 PLIP interactions:1 interactions with chain C, 4 interactions with chain A- Hydrophobic interactions: C:R.252, A:R.164
- Hydrogen bonds: A:H.290
- pi-Stacking: A:H.289, A:H.290
- 1 x GOL: GLYCEROL(Non-functional Binders)
- 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: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
DD
C
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.30 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 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
- 4 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
- 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
- 1 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)
- 7 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 19 x SO4: SULFATE ION(Non-functional Binders)
- 5 x NA: SODIUM ION(Non-functional Binders)
- 14 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 5 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)
- 1 x MFJ: [(R)-{[(2E,4Z,8Z)-dodeca-2,4,8-trien-1-yl]oxy}(naphthalen-1-yl)methyl]phosphonic acid(Non-covalent)
- 1 x GOL: GLYCEROL(Non-functional Binders)
- 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: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
DD
C