- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.65 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)
- 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(Post Translational Modification)
NAG-NAG-BMA-MAN.4: 9 residues within 4Å:- Chain A: S.590, S.593, A.594, N.597, Q.699
- Chain B: H.71, E.235, Y.236, R.313
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:E.235, B:R.313, B:R.313
- Water bridges: B:H.71, B:R.313
NAG-NAG-BMA-MAN.16: 9 residues within 4Å:- Chain A: H.71, E.235, Y.236, R.313
- Chain B: S.590, S.593, A.594, N.597, Q.699
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:E.235, A:R.313, A:R.313
- Water bridges: A:H.71, A:R.313
- 6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
NAG.5: 4 residues within 4Å:- Chain A: N.80, T.82, H.83, T.308
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:T.308
- Hydrogen bonds: A:T.82
NAG.6: 2 residues within 4Å:- Chain A: N.154, S.156
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:S.156
NAG.7: 4 residues within 4Å:- Chain A: W.205, N.418, F.524, Y.525
5 PLIP interactions:5 interactions with chain A- Hydrophobic interactions: A:W.205, A:Y.525
- Hydrogen bonds: A:W.205, A:F.524
- Water bridges: A:N.418
NAG.17: 4 residues within 4Å:- Chain B: N.80, T.82, H.83, T.308
2 PLIP interactions:2 interactions with chain B- Hydrophobic interactions: B:T.308
- Hydrogen bonds: B:T.82
NAG.18: 2 residues within 4Å:- Chain B: N.154, S.156
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:S.156
NAG.19: 4 residues within 4Å:- Chain B: W.205, N.418, F.524, Y.525
5 PLIP interactions:5 interactions with chain B- Hydrophobic interactions: B:W.205, B:Y.525
- Hydrogen bonds: B:W.205, B:F.524
- Water bridges: B:N.418
- 4 x ZN: ZINC ION(Non-covalent)
ZN.8: 5 residues within 4Å:- Chain A: D.346, E.384, H.512
- Ligands: ZN.9, JRG.12
5 PLIP interactions:4 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:D.346, A:E.384, A:E.384, A:H.512, H2O.22
ZN.9: 6 residues within 4Å:- Chain A: H.336, D.346, E.383, E.384, D.412
- Ligands: ZN.8
5 PLIP interactions:4 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:H.336, A:D.346, A:D.412, A:D.412, H2O.22
ZN.20: 5 residues within 4Å:- Chain B: D.346, E.384, H.512
- Ligands: ZN.21, JRG.24
5 PLIP interactions:4 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:D.346, B:E.384, B:E.384, B:H.512, H2O.44
ZN.21: 6 residues within 4Å:- Chain B: H.336, D.346, E.383, E.384, D.412
- Ligands: ZN.20
5 PLIP interactions:4 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:H.336, B:D.346, B:D.412, B:D.412, H2O.44
- 2 x CA: CALCIUM ION(Non-covalent)
CA.10: 4 residues within 4Å:- Chain A: T.228, Y.231, E.392, E.395
5 PLIP interactions:5 interactions with chain A- Metal complexes: A:T.228, A:Y.231, A:E.392, A:E.392, A:E.395
CA.22: 4 residues within 4Å:- Chain B: T.228, Y.231, E.392, E.395
5 PLIP interactions:5 interactions with chain B- Metal complexes: B:T.228, B:Y.231, B:E.392, B:E.392, B:E.395
- 2 x CL: CHLORIDE ION(Non-functional Binders)
- 2 x JRG: N~2~-{[(1S)-1-carboxy-3-(methylsulfanyl)propyl]carbamoyl}-N~6~-(4-iodobenzoyl)-L-lysine(Non-covalent)
JRG.12: 22 residues within 4Å:- Chain A: R.169, N.216, D.346, E.383, E.384, G.386, L.387, D.412, R.422, D.424, G.477, N.478, R.493, R.495, K.504, F.505, G.507, Y.511, H.512, K.658, Y.659
- Ligands: ZN.8
20 PLIP interactions:20 interactions with chain A- Hydrophobic interactions: A:Y.511
- Hydrogen bonds: A:E.384, A:G.477, A:G.477, A:N.478, A:Y.511
- Water bridges: A:N.216, A:D.346, A:R.422, A:R.493, A:R.493, A:R.495, A:K.504
- Salt bridges: A:R.169, A:R.493, A:R.495, A:H.512
- pi-Cation interactions: A:R.422, A:R.493
- Halogen bonds: A:R.422
JRG.24: 22 residues within 4Å:- Chain B: R.169, N.216, D.346, E.383, E.384, G.386, L.387, D.412, R.422, D.424, G.477, N.478, R.493, R.495, K.504, F.505, G.507, Y.511, H.512, K.658, Y.659
- Ligands: ZN.20
20 PLIP interactions:20 interactions with chain B- Hydrophobic interactions: B:Y.511
- Hydrogen bonds: B:E.384, B:G.477, B:G.477, B:N.478, B:Y.511
- Water bridges: B:N.216, B:D.346, B:R.422, B:R.493, B:R.493, B:R.495, B:K.504
- Salt bridges: B:R.169, B:R.493, B:R.495, B:H.512
- pi-Cation interactions: B:R.422, B:R.493
- Halogen bonds: B:R.422
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Plechanovova, A. et al., Novel Substrate-Based Inhibitors of Human Glutamate Carboxypeptidase II with Enhanced Lipophilicity. J.Med.Chem. (2011)
- Release Date
- 2011-10-05
- Peptides
- Glutamate carboxypeptidase 2: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.65 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)
- 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(Post Translational Modification)
- 6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 4 x ZN: ZINC ION(Non-covalent)
- 2 x CA: CALCIUM ION(Non-covalent)
- 2 x CL: CHLORIDE ION(Non-functional Binders)
- 2 x JRG: N~2~-{[(1S)-1-carboxy-3-(methylsulfanyl)propyl]carbamoyl}-N~6~-(4-iodobenzoyl)-L-lysine(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Plechanovova, A. et al., Novel Substrate-Based Inhibitors of Human Glutamate Carboxypeptidase II with Enhanced Lipophilicity. J.Med.Chem. (2011)
- Release Date
- 2011-10-05
- Peptides
- Glutamate carboxypeptidase 2: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
A