SMTL ID : 5ely.1

X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a hydroxamate inhibitor JHU242

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

homo-dimer

Ligands

6 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: 6 residues within 4Å: Chain A: N.22, Q.25, Q.41, S.44, Q.45, E.48 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.41 NAG-NAG.2: 5 residues within 4Å: Chain A: Y.73, E.83, I.84, F.85, N.86 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: S.418, L.419, N.422, P.540, Q.597 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.597 NAG-NAG.13: 6 residues within 4Å: Chain B: N.22, Q.25, Q.41, S.44, Q.45, E.48 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Q.41 NAG-NAG.14: 5 residues within 4Å: Chain B: Y.73, E.83, I.84, F.85, N.86 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 5 residues within 4Å: Chain B: S.418, L.419, N.422, P.540, Q.597 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.597

2 x NAG- NAG- BMA- MAN: alpha-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-MAN.4: 9 residues within 4Å: Chain A: S.577, S.580, A.581, N.584, Q.686 Chain B: H.58, E.222, Y.223, R.300 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.222, B:E.222, B:R.300, B:R.300 NAG-NAG-BMA-MAN.16: 9 residues within 4Å: Chain A: H.58, E.222, Y.223, R.300 Chain B: S.577, S.580, A.581, N.584, Q.686 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.222, A:E.222, A:R.300, A:R.300

4 x ZN: ZINC ION(Non-covalent)

ZN.5: 5 residues within 4Å: Chain A: D.333, E.371, H.499 Ligands: ZN.6, 5PU.11 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.333, A:E.371, A:E.371, A:H.499 ZN.6: 7 residues within 4Å: Chain A: H.323, D.333, E.370, E.371, D.399 Ligands: ZN.5, 5PU.11 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.323, A:D.333, A:D.399, A:D.399, H2O.9 ZN.17: 5 residues within 4Å: Chain B: D.333, E.371, H.499 Ligands: ZN.18, 5PU.23 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.333, B:E.371, B:E.371, B:H.499 ZN.18: 7 residues within 4Å: Chain B: H.323, D.333, E.370, E.371, D.399 Ligands: ZN.17, 5PU.23 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.323, B:D.333, B:D.399, B:D.399, H2O.27

2 x CA: CALCIUM ION(Non-covalent)

CA.7: 4 residues within 4Å: Chain A: T.215, Y.218, E.379, E.382 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:T.215, A:Y.218, A:E.379, A:E.379, A:E.382 CA.19: 4 residues within 4Å: Chain B: T.215, Y.218, E.379, E.382 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:T.215, B:Y.218, B:E.379, B:E.379, B:E.382

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

CL.8: 4 residues within 4Å: Chain A: N.397, D.399, R.480, R.526 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain B: N.397, D.399, R.480, R.526 Ligand excluded by PLIP

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

NAG.9: 4 residues within 4Å: Chain A: N.67, T.69, H.70, T.295 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.67, A:T.69, A:H.70 NAG.10: 4 residues within 4Å: Chain A: W.192, N.405, F.511, Y.512 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.192, A:Y.512 Hydrogen bonds: A:W.192, A:F.511 Water bridges: A:N.405, A:Y.518 NAG.21: 4 residues within 4Å: Chain B: N.67, T.69, H.70, T.295 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.67, B:T.69, B:H.70 NAG.22: 4 residues within 4Å: Chain B: W.192, N.405, F.511, Y.512 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.192, B:Y.512 Hydrogen bonds: B:W.192, B:F.511 Water bridges: B:N.405, B:Y.518

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

5PU.11: 16 residues within 4Å: Chain A: Y.180, H.323, D.333, E.370, E.371, D.399, G.464, N.465, R.480, G.494, Y.495, Y.498, H.499 Ligands: ZN.5, ZN.6, ACT.12 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.370, A:N.465, A:G.494, A:Y.495, A:Y.495 Water bridges: A:Q.200 Salt bridges: A:R.480 pi-Stacking: A:Y.498 5PU.23: 16 residues within 4Å: Chain B: Y.180, H.323, D.333, E.370, E.371, D.399, G.464, N.465, R.480, G.494, Y.495, Y.498, H.499 Ligands: ZN.17, ZN.18, ACT.24 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:E.370, B:N.465, B:G.494, B:Y.495, B:Y.495 Water bridges: B:Q.200 Salt bridges: B:R.480 pi-Stacking: B:Y.498

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

ACT.12: 7 residues within 4Å: Chain A: F.155, R.156, E.371, G.464, Y.498, H.499 Ligands: 5PU.11 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.155 Hydrogen bonds: A:N.203, A:Y.498 Water bridges: A:R.156, A:R.156, A:N.203, A:E.370, A:E.371 Salt bridges: A:R.156, A:H.499 ACT.24: 7 residues within 4Å: Chain B: F.155, R.156, E.371, G.464, Y.498, H.499 Ligands: 5PU.23 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.155 Hydrogen bonds: B:N.203, B:Y.498 Water bridges: B:R.156, B:R.156, B:N.203, B:E.370, B:E.371 Salt bridges: B:R.156, B:H.499

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