SMTL ID : 3ff3.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.37 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.15: 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 5 PLIP interactions: 5 interactions with chain A 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.154 NAG.4: 4 residues within 4Å: Chain A: W.203, N.416, F.522, Y.523 7 PLIP interactions: 7 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, A:N.416, A:D.443 NAG.16: 4 residues within 4Å: Chain B: N.78, T.80, N.81, I.306 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.81 Water bridges: B:N.78, B:N.78, B:Q.124 NAG.17: 2 residues within 4Å: Chain B: N.152, T.154 No protein-ligand interaction detected (PLIP) NAG.18: 4 residues within 4Å: Chain B: W.203, N.416, F.522, Y.523 6 PLIP interactions: 6 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, B:N.416

4 x ZN: ZINC ION(Non-covalent)

ZN.5: 5 residues within 4Å: Chain A: D.344, E.382, H.510 Ligands: ZN.6, GLU.9 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.344, A:E.382, A:H.510, H2O.35, H2O.35 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.7, H2O.35 ZN.19: 5 residues within 4Å: Chain B: D.344, E.382, H.510 Ligands: ZN.20, GLU.23 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.344, B:E.382, B:H.510, H2O.72, H2O.73 ZN.20: 5 residues within 4Å: Chain B: H.334, D.344, E.381, D.410 Ligands: ZN.19 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.334, B:D.344, B:D.410, H2O.44, H2O.72

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.21: 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.22: 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 GLU: GLUTAMIC ACID(Non-covalent)

GLU.9: 12 residues within 4Å: Chain A: R.167, N.214, E.381, E.382, G.384, L.385, G.475, Y.509, H.510, K.656, Y.657 Ligands: ZN.5 11 PLIP interactions: 7 interactions with chain A, 4 Ligand-Ligand interactions Hydrogen bonds: A:N.214, A:E.381, A:Y.509, E.9, E.9 Water bridges: A:K.656, E.9, E.9 Salt bridges: A:R.167, A:H.510, A:K.656 GLU.23: 12 residues within 4Å: Chain B: R.167, N.214, E.381, E.382, G.384, L.385, G.475, Y.509, H.510, K.656, Y.657 Ligands: ZN.19 12 PLIP interactions: 8 interactions with chain B, 4 Ligand-Ligand interactions Hydrogen bonds: B:N.214, B:E.381, B:Y.509, B:Y.657, E.23, E.23 Water bridges: B:K.656, E.23, E.23 Salt bridges: B:R.167, B:H.510, B:K.656

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 6 residues within 4Å: Chain A: K.436, E.437, I.438, P.439, K.448, S.449 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.448 Water bridges: A:W.16, A:E.437 GOL.11: 8 residues within 4Å: Chain A: Y.428, Y.432, S.460, E.462, L.466, P.467, R.468, I.469 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.432, A:E.462, A:I.469, A:I.469 Water bridges: A:S.460 GOL.12: 3 residues within 4Å: Chain A: F.590, S.591, K.594 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.590 Water bridges: A:N.595 GOL.13: 7 residues within 4Å: Chain A: L.636, G.637, L.638, P.639, K.687, H.688, I.691 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.687, A:H.688 Water bridges: A:G.640 GOL.14: 5 residues within 4Å: Chain A: E.25, K.28, S.29, R.32, F.516 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.28, A:K.28 GOL.24: 6 residues within 4Å: Chain B: K.436, E.437, I.438, P.439, K.448, S.449 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.448 Water bridges: B:W.16, B:E.437 GOL.25: 8 residues within 4Å: Chain B: Y.428, Y.432, S.460, E.462, L.466, P.467, R.468, I.469 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.469, B:I.469 Water bridges: B:Y.428, B:S.460 GOL.26: 3 residues within 4Å: Chain B: F.590, S.591, K.594 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.590 Water bridges: B:N.595 GOL.27: 7 residues within 4Å: Chain B: L.636, G.637, L.638, P.639, K.687, H.688, I.691 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Water bridges: A:Y.229, B:G.640 Hydrogen bonds: B:K.687, B:H.688 GOL.28: 5 residues within 4Å: Chain B: E.25, K.28, S.29, R.32, F.516 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.28, B:K.28

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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