SMTL ID : 7ov8.1

Crystal structure of pig purple acid phosphatase in complex with 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) and glycerol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 7 residues within 4Å: Chain A: H.87, D.88, A.89, N.124, A.127, K.133 Ligands: EDO.20 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.88

6 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.2: 5 residues within 4Å: Chain A: S.142, Y.144, Y.145, R.146, W.195 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.146, A:W.195 Salt bridges: A:R.146 EPE.3: 7 residues within 4Å: Chain A: H.121, G.170, N.171, D.174, R.184 Ligands: GOL.23, NA.33 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.121, A:N.171, A:D.174 Water bridges: A:R.184 EPE.4: 6 residues within 4Å: Chain A: R.35, K.67, T.68, L.69, G.70 Ligands: EDO.18 No protein-ligand interaction detected (PLIP) EPE.13: 2 residues within 4Å: Chain A: H.226, K.230 No protein-ligand interaction detected (PLIP) EPE.26: 5 residues within 4Å: Chain A: K.281 Ligands: GOL.22, GOL.27, GOL.28, EPE.29 No protein-ligand interaction detected (PLIP) EPE.29: 4 residues within 4Å: Chain A: K.281 Ligands: EPE.26, GOL.28, GOL.30 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.281

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: P.274, A.293, E.294 Ligands: GOL.9 Ligand excluded by PLIP GOL.6: 5 residues within 4Å: Chain A: R.280, V.282, N.284 Ligands: GOL.7, GOL.8 Ligand excluded by PLIP GOL.7: 7 residues within 4Å: Chain A: R.280, K.281, V.282, P.283 Ligands: GOL.6, GOL.8, GOL.30 Ligand excluded by PLIP GOL.8: 4 residues within 4Å: Chain A: P.283, N.284 Ligands: GOL.6, GOL.7 Ligand excluded by PLIP GOL.9: 7 residues within 4Å: Chain A: P.274, S.275, K.276, E.294 Ligands: GOL.5, GOL.10, GOL.11 Ligand excluded by PLIP GOL.10: 5 residues within 4Å: Chain A: E.221, D.273, S.275 Ligands: GOL.9, GOL.11 Ligand excluded by PLIP GOL.11: 5 residues within 4Å: Chain A: D.273, P.274, E.294 Ligands: GOL.9, GOL.10 Ligand excluded by PLIP GOL.12: 4 residues within 4Å: Chain A: Q.179, P.180, E.181, H.226 Ligand excluded by PLIP GOL.21: 6 residues within 4Å: Chain A: Q.178, H.222, H.250 Ligands: PO4.16, EDO.17, PGE.31 Ligand excluded by PLIP GOL.22: 4 residues within 4Å: Chain A: H.278, K.281 Ligands: EPE.26, GOL.27 Ligand excluded by PLIP GOL.23: 3 residues within 4Å: Chain A: R.184 Ligands: EPE.3, NA.33 Ligand excluded by PLIP GOL.24: 4 residues within 4Å: Chain A: P.49, F.50, E.96, D.100 Ligand excluded by PLIP GOL.25: 4 residues within 4Å: Chain A: F.175, R.182, P.183, R.184 Ligand excluded by PLIP GOL.27: 2 residues within 4Å: Ligands: GOL.22, EPE.26 Ligand excluded by PLIP GOL.28: 2 residues within 4Å: Ligands: EPE.26, EPE.29 Ligand excluded by PLIP GOL.30: 3 residues within 4Å: Chain A: K.281 Ligands: GOL.7, EPE.29 Ligand excluded by PLIP

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

FE.14: 7 residues within 4Å: Chain A: D.41, D.79, N.118, H.213, H.248 Ligands: FE.15, PO4.16 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.79, A:H.213, A:H.248, H2O.1 FE.15: 6 residues within 4Å: Chain A: D.41, D.79, Y.82, H.250 Ligands: FE.14, PO4.16 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.41, A:D.79, A:Y.82, A:H.250, H2O.1

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.16: 11 residues within 4Å: Chain A: D.79, Y.82, N.118, H.119, H.222, H.248, H.250 Ligands: FE.14, FE.15, GOL.21, PGE.31 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.118 Salt bridges: A:H.119, A:H.222, A:H.248, A:H.250

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

EDO.17: 10 residues within 4Å: Chain A: A.220, E.221, H.222, H.248, D.249, H.250, N.251, D.273, S.275 Ligands: GOL.21 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.221, A:H.248, A:H.250, A:N.251, A:D.273, A:D.273 EDO.18: 2 residues within 4Å: Chain A: T.68 Ligands: EPE.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.68 EDO.19: 2 residues within 4Å: Chain A: P.105, R.108 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.108 EDO.20: 3 residues within 4Å: Chain A: K.90, K.133 Ligands: NAG-NAG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.90, A:K.133

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

PGE.31: 7 residues within 4Å: Chain A: Y.82, F.83, H.119, L.122, D.173 Ligands: PO4.16, GOL.21 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.83, A:H.119, A:H.119

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

NA.32: 5 residues within 4Å: Chain A: S.132, S.135, K.136, W.138, N.139 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.138, A:N.139 NA.33: 2 residues within 4Å: Ligands: EPE.3, GOL.23 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Feder, D. et al., Rational Design of Potent Inhibitors of a Metallohydrolase Using a Fragment-Based Approach. Chemmedchem (2021)

Release Date

2022-03-23

Peptides

Tartrate-resistant acid phosphatase type 5: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Tartrate-resistant acid phosphatase type 5