SMTL ID : 7ov2.1

Crystal structure of pig purple acid phosphatase in complex with L-glutamine, (poly)ethylene glycol fragments and glycerol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- BMA: beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-BMA.1: 8 residues within 4Å: Chain A: H.60, D.61, A.62, N.97, A.100 Ligands: EDO.33, EDO.36, PGE.43 No protein-ligand interaction detected (PLIP)

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.2: 5 residues within 4Å: Chain A: Q.152, E.154, H.199, C.200 Ligands: PGE.40 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.154, A:C.200 1PE.5: 11 residues within 4Å: Chain A: S.105, K.106, I.107, S.108, K.109, R.110, W.111, N.112 Ligands: GOL.56, NA.63, GLN.71 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.109, A:R.110, A:N.112

1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.3: 8 residues within 4Å: Chain A: R.163, L.166, A.167, K.170, Q.204 Ligands: EDO.21, EDO.23, PGE.38 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.170 Water bridges: A:R.163, A:Q.204

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.4: 9 residues within 4Å: Chain A: V.202, K.203, L.206, P.207, T.210 Ligands: EDO.27, GOL.51, GOL.54, GLN.68 No protein-ligand interaction detected (PLIP) PG4.61: 4 residues within 4Å: Chain A: S.99 Ligands: PGE.43, CIT.60, GLN.62 2 PLIP interactions: 2 Ligand-Ligand interactions Hydrogen bonds: Q.62, Q.62

28 x GLN: GLUTAMINE(Non-covalent)

GLN.6: 8 residues within 4Å: Chain A: R.8, V.39, G.43, A.44, D.45, V.83 Ligands: GLN.7, EDO.35 10 PLIP interactions: 8 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:V.39 Hydrogen bonds: A:A.44, A:A.44, A:D.45, Q.6, Q.6 Water bridges: A:R.8, A:S.79, A:N.82 Salt bridges: A:R.8 GLN.7: 7 residues within 4Å: Chain A: T.4, P.5, I.6, R.8, P.125, R.126 Ligands: GLN.6 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:I.6, A:I.6, A:R.8, Q.7, Q.7 Salt bridges: A:R.126 GLN.8: 9 residues within 4Å: Chain A: L.42, Y.275, E.277, T.286, S.294, K.297 Ligands: GLN.19, EDO.24, GLN.76 7 PLIP interactions: 6 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:T.286 Hydrogen bonds: A:T.286, A:S.294, A:K.297, Q.8 Water bridges: A:K.297 Salt bridges: A:K.297 GLN.9: 8 residues within 4Å: Chain A: S.150, Q.151, Q.152, E.194, H.195, H.251 Ligands: GLN.10, GLN.13 9 PLIP interactions: 6 Ligand-Ligand interactions, 3 interactions with chain A Hydrogen bonds: Q.9, Q.9, Q.10, A:Q.151, A:H.195 Water bridges: Q.9, Q.9, Q.10 Salt bridges: A:K.250 GLN.10: 6 residues within 4Å: Chain A: K.250, H.251, R.253, K.254 Ligands: GLN.9, EDO.30 8 PLIP interactions: 6 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:K.250, A:K.254, A:K.254, Q.9 Water bridges: A:H.251, Q.9 Salt bridges: A:H.251, A:K.254 GLN.11: 9 residues within 4Å: Chain A: L.209, T.210, K.213, V.214, T.215, N.232, G.233, L.234, P.301 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.209, A:T.215 Water bridges: A:K.213, A:K.213 Salt bridges: A:K.213 GLN.12: 9 residues within 4Å: Chain A: V.139, T.140, G.143, N.144, P.156, R.157, N.158, L.161 Ligands: CIT.60 8 PLIP interactions: 7 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:T.140 Hydrogen bonds: A:T.140, A:G.143, A:N.144, A:R.157, A:N.158 Water bridges: A:D.147, Q.16 GLN.13: 10 residues within 4Å: Chain A: Q.151, E.194, H.195, D.246, K.250 Ligands: GLN.9, PO4.20, EDO.29, PGE.42, GOL.53 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:Q.151, A:D.246 Water bridges: A:E.194, A:D.246, Q.13 Salt bridges: A:K.250 GLN.14: 6 residues within 4Å: Chain A: R.27, F.244, M.245 Ligands: GLN.18, PGE.42, GOL.53 6 PLIP interactions: 6 interactions with chain A, Hydrogen bonds: A:M.245 Water bridges: A:R.27, A:R.27, A:D.246, A:D.246 Salt bridges: A:R.27 GLN.15: 5 residues within 4Å: Chain A: R.27, E.267, N.268, L.270 Ligands: GOL.47 4 PLIP interactions: 2 Ligand-Ligand interactions, 2 interactions with chain A Hydrogen bonds: Q.15, Q.15, A:E.267 Salt bridges: A:R.27 GLN.16: 6 residues within 4Å: Chain A: D.147, F.148, R.155, P.156, R.157 Ligands: PGE.45 9 PLIP interactions: 6 interactions with chain A, 3 Ligand-Ligand interactions Hydrophobic interactions: A:D.147, A:R.157 Hydrogen bonds: A:D.147, A:R.155, A:R.155, Q.16, Q.16 Salt bridges: A:R.157 Water bridges: Q.12 GLN.17: 4 residues within 4Å: Chain A: N.128, D.179, R.302, R.305 8 PLIP interactions: 4 interactions with chain A, 4 Ligand-Ligand interactions Hydrogen bonds: A:D.179, A:R.302, A:R.305, Q.17, Q.17, Q.17, Q.17 Water bridges: A:N.128 GLN.18: 10 residues within 4Å: Chain A: Y.55, F.56, H.92, H.223, F.244 Ligands: GLN.14, PO4.20, EDO.28, EDO.29, GLN.66 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.244 Hydrogen bonds: A:H.92 Salt bridges: A:H.92 GLN.19: 9 residues within 4Å: Chain A: E.277, I.278, T.279, E.282, M.283, S.284, K.297 Ligands: GLN.8, EDO.24 11 PLIP interactions: 2 Ligand-Ligand interactions, 9 interactions with chain A Hydrogen bonds: Q.19, Q.19, A:E.277, A:T.279, A:S.284, A:S.284 Hydrophobic interactions: A:T.279, A:E.282 Water bridges: A:K.297, A:K.297 Salt bridges: A:K.297 GLN.59: 2 residues within 4Å: Chain A: T.164 Ligands: GLN.62 1 PLIP interactions: 1 Ligand-Ligand interactions Hydrogen bonds: Q.62 GLN.62: 8 residues within 4Å: Chain A: V.98, S.99, I.102, P.116, L.161 Ligands: GLN.59, CIT.60, PG4.61 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:P.116 Hydrogen bonds: A:S.99, A:S.99, Q.59 Water bridges: A:Y.117, A:Y.117 GLN.66: 8 residues within 4Å: Chain A: F.56, T.57, H.92, D.146 Ligands: GLN.18, EDO.28, GOL.52, GLN.74 7 PLIP interactions: 3 Ligand-Ligand interactions, 4 interactions with chain A Hydrogen bonds: Q.66, Q.66, Q.74 Hydrophobic interactions: A:F.56, A:T.57 Water bridges: A:F.56 Salt bridges: A:H.92 GLN.67: 4 residues within 4Å: Chain A: R.119, L.120, R.121 Ligands: GLN.72 9 PLIP interactions: 6 interactions with chain A, 3 Ligand-Ligand interactions Hydrophobic interactions: A:L.120 Hydrogen bonds: A:R.121, A:R.121 Water bridges: A:N.112, A:R.119, Q.67, Q.67, Q.72 Salt bridges: A:R.119 GLN.68: 10 residues within 4Å: Chain A: W.190, V.202, K.203, L.206, E.231, Y.259 Ligands: PG4.4, GOL.46, GOL.49, GOL.54 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:W.190 Hydrogen bonds: A:E.231 Salt bridges: A:K.203 Water bridges: Q.68 GLN.69: 4 residues within 4Å: Chain A: K.254 Ligands: EDO.30, GOL.46, GOL.49 9 PLIP interactions: 5 interactions with chain A, 4 Ligand-Ligand interactions Hydrophobic interactions: A:K.254 Water bridges: A:K.254, A:K.254 Salt bridges: A:H.199, A:K.254 Hydrogen bonds: Q.69, Q.69, Q.69, Q.69 GLN.70: 4 residues within 4Å: Chain A: N.268, S.269, E.289 Ligands: EDO.32 3 PLIP interactions: 3 interactions with chain A, Hydrogen bonds: A:E.289 Water bridges: A:L.270, A:L.270 GLN.71: 7 residues within 4Å: Chain A: E.72, D.73, S.76, R.81, R.110 Ligands: 1PE.5, GOL.56 6 PLIP interactions: 4 Ligand-Ligand interactions, 2 interactions with chain A Hydrogen bonds: Q.71, Q.71, Q.71, Q.71, A:D.73 Salt bridges: A:R.110 GLN.72: 5 residues within 4Å: Chain A: P.114, S.115, Y.118, R.119 Ligands: GLN.67 7 PLIP interactions: 6 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:P.114, A:Y.118 Hydrogen bonds: A:S.115, A:Y.117, A:R.119 Water bridges: A:R.119, Q.67 GLN.73: 1 residues within 4Å: Chain A: K.203 2 PLIP interactions: 2 interactions with chain A, Water bridges: A:K.203 Salt bridges: A:K.203 GLN.74: 6 residues within 4Å: Chain A: D.146, D.147 Ligands: PGE.45, GOL.50, GOL.52, GLN.66 5 PLIP interactions: 4 Ligand-Ligand interactions, 1 interactions with chain A Hydrogen bonds: Q.66, Q.66, Q.74 Water bridges: Q.66 Salt bridges: A:R.157 GLN.75: 5 residues within 4Å: Chain A: R.261, F.262, L.295, F.296 Ligands: GLN.76 7 PLIP interactions: 1 interactions with chain A, 6 Ligand-Ligand interactions Hydrophobic interactions: A:F.262 Hydrogen bonds: Q.75, Q.75, Q.75, Q.75, Q.76, Q.76 GLN.76: 8 residues within 4Å: Chain A: S.294, L.295, F.296, K.297 Ligands: GLN.8, EDO.24, GLN.75, GLN.77 4 PLIP interactions: 3 Ligand-Ligand interactions, 1 interactions with chain A Hydrogen bonds: Q.75, Q.75, Q.77 Water bridges: A:K.297 GLN.77: 3 residues within 4Å: Chain A: K.293, S.294 Ligands: GLN.76 6 PLIP interactions: 4 Ligand-Ligand interactions, 2 interactions with chain A Hydrogen bonds: Q.76, Q.77, Q.77, A:S.294 Water bridges: Q.77 Hydrophobic interactions: A:K.293

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

PO4.20: 13 residues within 4Å: Chain A: D.14, D.52, Y.55, N.91, H.92, H.195, H.221, H.223 Ligands: GLN.13, GLN.18, EDO.29, FE.64, FE.65 11 PLIP interactions: 2 Ligand-Ligand interactions, 9 interactions with chain A Hydrogen bonds: Q.18, Q.18, A:D.14, A:N.91, A:N.91 Water bridges: A:H.195, A:H.223 Salt bridges: A:H.92, A:H.195, A:H.221, A:H.223

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

EDO.21: 4 residues within 4Å: Chain A: P.207, L.208, T.211 Ligands: P6G.3 Ligand excluded by PLIP EDO.22: 1 residues within 4Å: Chain A: T.211 Ligand excluded by PLIP EDO.23: 1 residues within 4Å: Ligands: P6G.3 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain A: K.297 Ligands: GLN.8, GLN.19, GLN.76 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain A: T.57, G.58, V.59, H.60, G.96 Ligands: GOL.50 Ligand excluded by PLIP EDO.26: 2 residues within 4Å: Chain A: G.292 Ligands: PGE.41 Ligand excluded by PLIP EDO.27: 2 residues within 4Å: Chain A: P.207 Ligands: PG4.4 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain A: Q.151 Ligands: GLN.18, GOL.52, GLN.66 Ligand excluded by PLIP EDO.29: 8 residues within 4Å: Chain A: N.91, S.145, D.146, Q.151, H.195 Ligands: GLN.13, GLN.18, PO4.20 Ligand excluded by PLIP EDO.30: 3 residues within 4Å: Chain A: K.254 Ligands: GLN.10, GLN.69 Ligand excluded by PLIP EDO.31: 3 residues within 4Å: Chain A: K.106, I.107 Ligands: GOL.56 Ligand excluded by PLIP EDO.32: 3 residues within 4Å: Chain A: S.291, K.293 Ligands: GLN.70 Ligand excluded by PLIP EDO.33: 4 residues within 4Å: Chain A: A.62, A.103 Ligands: NAG-NAG-BMA-BMA.1, NAG-NAG-BMA-BMA.1 Ligand excluded by PLIP EDO.34: 4 residues within 4Å: Chain A: K.65, Q.68, E.69, D.73 Ligand excluded by PLIP EDO.35: 5 residues within 4Å: Chain A: A.44, D.45, N.82, P.84 Ligands: GLN.6 Ligand excluded by PLIP EDO.36: 2 residues within 4Å: Ligands: NAG-NAG-BMA-BMA.1, NAG-NAG-BMA-BMA.1 Ligand excluded by PLIP EDO.37: 4 residues within 4Å: Chain A: I.102, S.105, K.106, P.114 Ligand excluded by PLIP

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

PGE.38: 5 residues within 4Å: Chain A: A.160, R.163, T.164, A.167 Ligands: P6G.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.163 PGE.39: 4 residues within 4Å: Chain A: K.249, L.252, L.260, H.263 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.249, A:H.263 PGE.40: 6 residues within 4Å: Chain A: L.141, P.156, L.166, C.200, Q.204 Ligands: 1PE.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.204 Water bridges: A:Q.204 PGE.41: 8 residues within 4Å: Chain A: A.30, K.33, A.34, T.37, T.38, A.290, G.292 Ligands: EDO.26 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.37 PGE.42: 6 residues within 4Å: Chain A: E.194, D.246, S.248 Ligands: GLN.13, GLN.14, GOL.53 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.248 Water bridges: A:S.248, A:S.248 PGE.43: 6 residues within 4Å: Chain A: H.60, G.96, N.97 Ligands: NAG-NAG-BMA-BMA.1, CIT.60, PG4.61 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.60 PGE.44: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PGE.45: 3 residues within 4Å: Chain A: R.157 Ligands: GLN.16, GLN.74 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.157

13 x GOL: GLYCEROL(Non-functional Binders)

GOL.46: 7 residues within 4Å: Chain A: R.253, K.254, V.255, P.256 Ligands: GOL.49, GLN.68, GLN.69 No protein-ligand interaction detected (PLIP) GOL.47: 4 residues within 4Å: Chain A: T.25, A.26, R.27 Ligands: GLN.15 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.26, A:R.27 Water bridges: A:R.27, A:R.27 GOL.48: 5 residues within 4Å: Chain A: A.36, T.37, K.40, D.77, P.78 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.36, A:S.79 Water bridges: A:K.40 GOL.49: 7 residues within 4Å: Chain A: W.190, H.199, V.202, K.254 Ligands: GOL.46, GLN.68, GLN.69 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.199, A:K.254 Water bridges: A:K.203, A:K.203 GOL.50: 3 residues within 4Å: Chain A: L.95 Ligands: EDO.25, GLN.74 No protein-ligand interaction detected (PLIP) GOL.51: 4 residues within 4Å: Chain A: T.210, N.232 Ligands: PG4.4, GOL.54 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.232 Water bridges: A:T.210 GOL.52: 7 residues within 4Å: Chain A: D.146, F.148, V.149, Q.151 Ligands: EDO.28, GLN.66, GLN.74 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.151 GOL.53: 3 residues within 4Å: Ligands: GLN.13, GLN.14, PGE.42 No protein-ligand interaction detected (PLIP) GOL.54: 10 residues within 4Å: Chain A: W.190, L.206, T.210, D.230, E.231, N.232, Y.259 Ligands: PG4.4, GOL.51, GLN.68 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.230, A:E.231, A:N.232 GOL.55: 7 residues within 4Å: Chain A: L.252, V.255, P.256, N.257, G.258, Y.259, L.260 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.255, A:G.258, A:Y.259, A:L.260 GOL.56: 7 residues within 4Å: Chain A: Q.68, E.72, Y.104, I.107 Ligands: 1PE.5, EDO.31, GLN.71 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.68, A:E.72 GOL.57: 6 residues within 4Å: Chain A: R.81, N.82, V.83, P.84, K.109, R.110 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.82 Water bridges: A:K.109 GOL.58: 5 residues within 4Å: Chain A: D.147, F.148, V.149, S.150, E.154 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.149, A:S.150, A:E.154

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.60: 9 residues within 4Å: Chain A: H.94, G.96, N.97, V.98, S.99 Ligands: GLN.12, PGE.43, PG4.61, GLN.62 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:V.98, A:S.99, A:S.99 Salt bridges: A:H.94 Water bridges: Q.62

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

NA.63: 5 residues within 4Å: Chain A: S.105, S.108, K.109, W.111 Ligands: 1PE.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.105

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

FE.64: 6 residues within 4Å: Chain A: D.14, D.52, Y.55, H.223 Ligands: PO4.20, FE.65 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.14, A:D.52, A:Y.55, A:H.223, H2O.1 FE.65: 7 residues within 4Å: Chain A: D.14, D.52, N.91, H.186, H.221 Ligands: PO4.20, FE.64 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.52, A:H.186, A:H.221, H2O.1

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

2022-01-12

Peptides

Tartrate-resistant acid phosphatase type 5: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Tartrate-resistant acid phosphatase type 5

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