SMTL ID : 4p4f.1

X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a phosphoramidate inhibitor NC-2-40

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 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: 5 residues within 4Å: Chain A: N.33, Q.36, Q.52, S.55, Q.56 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.55 NAG-NAG.2: 4 residues within 4Å: Chain A: N.78, T.80, H.81, T.306 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: Y.84, E.94, I.95, N.97 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 5 residues within 4Å: Chain B: N.33, Q.36, Q.52, S.55, Q.56 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.55 NAG-NAG.14: 4 residues within 4Å: Chain B: N.78, T.80, H.81, T.306 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain B: Y.84, E.94, I.95, N.97 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA.4: 5 residues within 4Å: Chain A: S.429, L.430, N.433, P.551, Q.608 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.609 Water bridges: A:Q.608 NAG-NAG-BMA.16: 5 residues within 4Å: Chain B: S.429, L.430, N.433, P.551, Q.608 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.609 Water bridges: B:Q.608

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.5: 9 residues within 4Å: Chain A: S.588, S.591, A.592, N.595, Q.697 Chain B: H.69, E.233, Y.234, R.311 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.233, B:R.311, B:R.311 Water bridges: B:H.69, B:D.71, B:R.311 NAG-NAG-BMA-MAN.17: 9 residues within 4Å: Chain A: H.69, E.233, Y.234, R.311 Chain B: S.588, S.591, A.592, N.595, Q.697 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.233, A:R.311, A:R.311 Water bridges: A:H.69, A:D.71, A:R.311

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

NAG.6: 2 residues within 4Å: Chain A: N.152, S.154 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.152, A:S.154 NAG.7: 4 residues within 4Å: Chain A: W.203, N.416, F.522, Y.523 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.203, A:Y.523 Hydrogen bonds: A:W.203, A:F.522 Water bridges: A:N.416 NAG.18: 2 residues within 4Å: Chain B: N.152, S.154 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.152, B:S.154 NAG.19: 4 residues within 4Å: Chain B: W.203, N.416, F.522, Y.523 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.203, B:Y.523 Hydrogen bonds: B:W.203, B:F.522 Water bridges: B:N.416

4 x ZN: ZINC ION(Non-covalent)

ZN.8: 6 residues within 4Å: Chain A: D.344, E.382, Y.509, H.510 Ligands: ZN.9, 2GB.12 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.344, A:E.382, A:E.382, A:H.510 ZN.9: 7 residues within 4Å: Chain A: H.334, D.344, E.381, E.382, D.410 Ligands: ZN.8, 2GB.12 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.334, A:D.344, A:D.410, A:D.410 ZN.20: 6 residues within 4Å: Chain B: D.344, E.382, Y.509, H.510 Ligands: ZN.21, 2GB.24 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.344, B:E.382, B:E.382, B:H.510 ZN.21: 7 residues within 4Å: Chain B: H.334, D.344, E.381, E.382, D.410 Ligands: ZN.20, 2GB.24 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.334, B:D.344, B:D.410, B:D.410

2 x CA: CALCIUM ION(Non-covalent)

CA.10: 4 residues within 4Å: Chain A: T.226, Y.229, E.390, E.393 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.226, A:Y.229, A:E.390, A:E.393, H2O.5 CA.22: 4 residues within 4Å: Chain B: T.226, Y.229, E.390, E.393 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.226, B:Y.229, B:E.390, B:E.393, H2O.27

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

CL.11: 4 residues within 4Å: Chain A: N.408, D.410, R.491, R.537 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Chain B: N.408, D.410, R.491, R.537 Ligand excluded by PLIP

2 x 2GB: N-[(S)-(biphenyl-4-ylmethoxy)(hydroxy)phosphoryl]-L-glutamic acid(Non-covalent)

2GB.12: 25 residues within 4Å: Chain A: R.167, N.214, H.334, D.344, E.381, E.382, G.384, L.385, D.410, E.414, R.420, G.475, N.476, K.496, N.501, K.502, F.503, G.505, Y.506, Y.509, H.510, K.656, Y.657 Ligands: ZN.8, ZN.9 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.385, A:E.414, A:E.414, A:K.496, A:Y.506, A:Y.509 Hydrogen bonds: A:N.214, A:E.381, A:G.475, A:N.476, A:Y.509 Salt bridges: A:R.167, A:H.510, A:K.656 pi-Stacking: A:Y.657 2GB.24: 25 residues within 4Å: Chain B: R.167, N.214, H.334, D.344, E.381, E.382, G.384, L.385, D.410, E.414, R.420, G.475, N.476, K.496, N.501, K.502, F.503, G.505, Y.506, Y.509, H.510, K.656, Y.657 Ligands: ZN.20, ZN.21 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:L.385, B:E.414, B:E.414, B:K.496, B:Y.506, B:Y.509 Hydrogen bonds: B:N.214, B:E.381, B:G.475, B:N.476, B:Y.509 Salt bridges: B:R.167, B:H.510, B:K.656 pi-Stacking: B:Y.657

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Novakova, Z. et al., Design of composite inhibitors targeting glutamate carboxypeptidase II: the importance of effector functionalities. Febs J. (2016)

Release Date

2015-05-20

Peptides

Glutamate carboxypeptidase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glutamate carboxypeptidase 2

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