SMTL ID : 3fed.1

The high resolution structure of human glutamate carboxypeptidase III (GCPIII/NAALADase II) in complex with a transition state analog of Glu-Glu

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.29 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 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.69

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 6 PLIP interactions: 6 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:Q.124 NAG.3: 2 residues within 4Å: Chain A: N.152, T.154 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.152, A:T.154 Water bridges: 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 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.306 Hydrogen bonds: B:N.81 Water bridges: B:N.78, B:N.78, B:Q.124 NAG.12: 2 residues within 4Å: Chain B: N.152, T.154 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.152 Water bridges: B:T.154 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: 6 residues within 4Å: Chain A: D.344, E.382, Y.509, H.510 Ligands: ZN.6, BIX.9 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.344, A:E.382, A:E.382, A:H.510 ZN.6: 6 residues within 4Å: Chain A: H.334, D.344, E.381, D.410 Ligands: ZN.5, BIX.9 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.334, A:D.344, A:D.410, A:D.410, H2O.22 ZN.14: 6 residues within 4Å: Chain B: D.344, E.382, Y.509, H.510 Ligands: ZN.15, BIX.18 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.344, B:E.382, B:E.382, B:H.510 ZN.15: 6 residues within 4Å: Chain B: H.334, D.344, E.381, D.410 Ligands: ZN.14, BIX.18 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.334, B:D.344, B:D.410, B:D.410, H2O.55

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 BIX: (2S)-2-{[(S)-[(3S)-3-amino-3-carboxypropyl](hydroxy)phosphoryl]methyl}pentanedioic acid(Non-covalent)

BIX.9: 18 residues within 4Å: Chain A: R.167, N.214, H.334, D.344, E.381, E.382, G.384, D.410, S.474, G.475, R.491, R.493, Y.509, H.510, K.656, Y.657 Ligands: ZN.5, ZN.6 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.657 Hydrogen bonds: A:N.214, A:N.214, A:E.382, A:Y.509 Water bridges: A:R.493, A:S.505, A:Y.509, A:K.656 Salt bridges: A:R.167, A:R.491, A:R.493, A:H.510, A:K.656 BIX.18: 18 residues within 4Å: Chain B: R.167, N.214, H.334, D.344, E.381, E.382, G.384, D.410, S.474, G.475, R.491, R.493, Y.509, H.510, K.656, Y.657 Ligands: ZN.14, ZN.15 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:Y.657 Hydrogen bonds: B:N.214, B:N.214, B:E.382, B:Y.509, B:Y.509, B:Y.657 Water bridges: B:E.382, B:R.493, B:S.505, B:Y.509, B:K.656 Salt bridges: B:R.167, B:R.491, B:R.493, B:H.510, B:K.656

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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