SMTL ID : 4p44.1

X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a phosphoramidate inhibitor JRB-4-81

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

3 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 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.52 Hydrogen bonds: A:S.55 NAG-NAG.2: 4 residues within 4Å: Chain A: Y.84, E.94, I.95, N.97 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: S.429, L.430, N.433, P.551 No protein-ligand interaction detected (PLIP)

1 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: 5 residues within 4Å: Chain A: S.588, S.591, A.592, N.595, Q.697 No protein-ligand interaction detected (PLIP)

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

NAG.5: 4 residues within 4Å: Chain A: N.78, T.80, H.81, T.306 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.306 Hydrogen bonds: A:T.80 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

2 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, 2F7.12 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, 2F7.12 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.334, A:D.344, A:D.410, A:D.410

1 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: 5 interactions with chain A Metal complexes: A:T.226, A:Y.229, A:E.390, A:E.390, A:E.393

1 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

1 x 2F7: N-(4-fluorobenzoyl)-L-alloisoleucyl-O-[(S)-{[(1S)-1,3-dicarboxypropyl]amino}(hydroxy)phosphoryl]-L-serine(Non-covalent)

2F7.12: 25 residues within 4Å: Chain A: G.163, K.164, V.165, R.167, N.214, H.334, D.344, E.381, E.382, G.384, L.385, D.410, E.414, G.475, N.476, R.491, R.493, G.505, Y.506, Y.509, H.510, K.656, Y.657 Ligands: ZN.8, ZN.9 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.506, A:Y.506, A:Y.509, A:Y.657, A:Y.657 Hydrogen bonds: A:N.214, A:E.381, A:N.476, A:Y.509 Water bridges: A:S.411, A:R.493, A:K.656 Salt bridges: A:R.167, A:R.491, A:H.510, A:K.656

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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Glutamate carboxypeptidase 2

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