SMTL ID : 5d29.1

X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a hydroxamate inhibitor JHU241

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

4 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: 4 residues within 4Å: Chain A: N.21, Q.40, S.43, Q.44 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: S.417, L.418, N.421, P.539 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain B: N.21, Q.40, S.43, Q.44 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain B: S.417, L.418, N.421, P.539 No protein-ligand interaction detected (PLIP)

2 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.3: 9 residues within 4Å: Chain A: S.576, S.579, A.580, N.583, Q.685 Chain B: H.57, E.221, Y.222, R.299 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-BMA.16: 9 residues within 4Å: Chain A: H.57, E.221, Y.222, R.299 Chain B: S.576, S.579, A.580, N.583, Q.685 No protein-ligand interaction detected (PLIP)

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

NAG.4: 4 residues within 4Å: Chain A: N.66, T.68, H.69, T.294 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.294 Hydrogen bonds: A:T.68 Water bridges: A:H.69 NAG.5: 4 residues within 4Å: Chain A: Y.72, E.82, I.83, N.85 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.72, A:E.82, A:E.82, A:N.85 NAG.6: 2 residues within 4Å: Chain A: N.140, S.142 No protein-ligand interaction detected (PLIP) NAG.7: 4 residues within 4Å: Chain A: W.191, N.404, F.510, Y.511 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.191, A:Y.511 Hydrogen bonds: A:W.191, A:N.404, A:F.510 NAG.17: 4 residues within 4Å: Chain B: N.66, T.68, H.69, T.294 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.294 Hydrogen bonds: B:T.68 Water bridges: B:H.69 NAG.18: 4 residues within 4Å: Chain B: Y.72, E.82, I.83, N.85 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.72, B:E.82, B:E.82, B:N.85 NAG.19: 2 residues within 4Å: Chain B: N.140, S.142 No protein-ligand interaction detected (PLIP) NAG.20: 4 residues within 4Å: Chain B: W.191, N.404, F.510, Y.511 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.191, B:Y.511 Hydrogen bonds: B:W.191, B:N.404, B:F.510

4 x ZN: ZINC ION(Non-covalent)

ZN.8: 6 residues within 4Å: Chain A: D.332, E.370, Y.497, H.498 Ligands: ZN.9, 5Q1.13 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.332, A:E.370, A:E.370, A:H.498 ZN.9: 7 residues within 4Å: Chain A: H.322, D.332, E.369, E.370, D.398 Ligands: ZN.8, 5Q1.13 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.322, A:D.332, A:D.398, A:D.398, H2O.3 ZN.21: 6 residues within 4Å: Chain B: D.332, E.370, Y.497, H.498 Ligands: ZN.22, 5Q1.26 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.332, B:E.370, B:E.370, B:H.498 ZN.22: 7 residues within 4Å: Chain B: H.322, D.332, E.369, E.370, D.398 Ligands: ZN.21, 5Q1.26 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.322, B:D.332, B:D.398, B:D.398, H2O.17

2 x CA: CALCIUM ION(Non-covalent)

CA.10: 4 residues within 4Å: Chain A: T.214, Y.217, E.378, E.381 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.214, A:Y.217, A:E.378, A:E.381, H2O.3 CA.23: 4 residues within 4Å: Chain B: T.214, Y.217, E.378, E.381 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.214, B:Y.217, B:E.378, B:E.381, H2O.17

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.11: 4 residues within 4Å: Chain A: N.396, D.398, R.479, R.525 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain B: N.396, D.398, R.479, R.525 Ligand excluded by PLIP

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

ACT.12: 8 residues within 4Å: Chain A: F.154, R.155, E.369, E.370, Y.497, H.498, Y.645 Ligands: 5Q1.13 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.497 Water bridges: A:N.202 Salt bridges: A:R.155, A:H.498 ACT.25: 8 residues within 4Å: Chain B: F.154, R.155, E.369, E.370, Y.497, H.498, Y.645 Ligands: 5Q1.26 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.497 Water bridges: B:N.202 Salt bridges: B:R.155, B:H.498

2 x 5Q1: 4-[(2~{S})-2-carboxy-5-(oxidanylamino)-5-oxidanylidene-pentyl]benzoic acid(Non-covalent)

5Q1.13: 17 residues within 4Å: Chain A: Y.179, H.322, D.332, E.369, E.370, D.398, G.463, N.464, R.479, G.493, Y.494, Y.497, H.498, Y.645 Ligands: ZN.8, ZN.9, ACT.12 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.645, A:Y.645 Hydrogen bonds: A:E.369, A:N.464, A:Y.494, A:Y.494 Water bridges: A:Q.199, A:D.332, A:D.398, A:S.399, A:S.399, A:R.479 Salt bridges: A:R.479 pi-Stacking: A:Y.497 5Q1.26: 17 residues within 4Å: Chain B: Y.179, H.322, D.332, E.369, E.370, D.398, G.463, N.464, R.479, G.493, Y.494, Y.497, H.498, Y.645 Ligands: ZN.21, ZN.22, ACT.25 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:Y.645, B:Y.645 Hydrogen bonds: B:E.369, B:N.464, B:Y.494, B:Y.494 Water bridges: B:Q.199, B:D.332, B:D.398, B:S.399, B:S.399, B:R.479 Salt bridges: B:R.479 pi-Stacking: B:Y.497

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Novakova, Z. et al., Unprecedented Binding Mode of Hydroxamate-Based Inhibitors of Glutamate Carboxypeptidase II: Structural Characterization and Biological Activity. J.Med.Chem. (2016)

Release Date

2016-04-27

Peptides

Glutamate carboxypeptidase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glutamate carboxypeptidase 2

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