SMTL ID : 3fee.1

The high resolution structure of human glutamate carboxypeptidase III (GCPIII/NAALADase II) in complex with quisqualic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

homo-dimer

Ligands

2 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: 7 residues within 4Å: Chain A: S.588, S.591, A.592, N.595, Q.697 Chain B: E.233, Y.234 1 PLIP interactions: 1 interactions with chain B Water bridges: B:H.69 NAG-NAG.10: 7 residues within 4Å: Chain A: E.233, Y.234 Chain B: S.588, S.591, A.592, N.595, Q.697 2 PLIP interactions: 2 interactions with chain A Water bridges: A:H.69, A:E.233

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

NAG.2: 4 residues within 4Å: Chain A: N.78, T.80, N.81, I.306 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.306 Hydrogen bonds: A:T.80, A:N.81 Water bridges: A:N.78, A:N.78, A:N.78, A:Q.124 NAG.3: 2 residues within 4Å: Chain A: N.152, T.154 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.152, A:T.154 NAG.4: 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.11: 4 residues within 4Å: Chain B: N.78, T.80, N.81, I.306 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.306 Hydrogen bonds: B:N.81 Water bridges: B:N.78, B:N.78, B:N.78, B:Q.124 NAG.12: 2 residues within 4Å: Chain B: N.152, T.154 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.152 NAG.13: 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.5: 4 residues within 4Å: Chain A: D.344, E.382, H.510 Ligands: ZN.6 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.344, A:E.382, A:H.510, H2O.31, H2O.31 ZN.6: 5 residues within 4Å: Chain A: H.334, D.344, E.381, D.410 Ligands: ZN.5 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.334, A:D.344, A:D.410, H2O.19, H2O.31 ZN.14: 4 residues within 4Å: Chain B: D.344, E.382, H.510 Ligands: ZN.15 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.344, B:E.382, B:H.510, H2O.63, H2O.63 ZN.15: 5 residues within 4Å: Chain B: H.334, D.344, E.381, D.410 Ligands: ZN.14 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.334, B:D.344, B:D.410, H2O.51, H2O.63

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

CL.7: 4 residues within 4Å: Chain A: N.408, D.410, R.491, R.537 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain B: N.408, D.410, R.491, R.537 Ligand excluded by PLIP

2 x CA: CALCIUM ION(Non-covalent)

CA.8: 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 CA.17: 4 residues within 4Å: Chain B: T.226, Y.229, E.390, E.393 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:T.226, B:Y.229, B:E.390, B:E.390, B:E.393

2 x QUS: (S)-2-AMINO-3-(3,5-DIOXO-[1,2,4]OXADIAZOLIDIN-2-YL)-PROPIONIC ACID(Non-covalent)

QUS.9: 13 residues within 4Å: Chain A: F.166, R.167, N.214, E.381, E.382, G.384, L.385, S.474, G.475, Y.509, H.510, K.656, Y.657 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.214, A:E.381, A:E.382, A:G.475, A:Y.509, A:K.656, A:K.656 Salt bridges: A:R.167, A:H.510 QUS.18: 13 residues within 4Å: Chain B: F.166, R.167, N.214, E.381, E.382, G.384, L.385, S.474, G.475, Y.509, H.510, K.656, Y.657 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:N.214, B:E.381, B:E.382, B:E.382, B:G.475, B:Y.509, B:K.656, B:K.656, B:Y.657 Salt bridges: B:R.167, B:H.510

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hlouchova, K. et al., Structural insight into the evolutionary and pharmacologic homology of glutamate carboxypeptidases II and III. Febs J. (2009)

Release Date

2009-08-25

Peptides

Glutamate carboxypeptidase III: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glutamate carboxypeptidase III

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