SMTL ID : 3fec.1

Crystal structure of human Glutamate Carboxypeptidase III (GCPIII/NAALADase II), pseudo-unliganded

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.49 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.13: 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

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.2: 14 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.6, GOL.10, MPO.12 14 PLIP interactions: 10 interactions with chain A, 4 Ligand-Ligand interactions Hydrogen bonds: A:N.214, A:Y.509, A:Y.657, E.2, E.2 Water bridges: A:H.334, A:D.344, A:E.381, A:D.410, E.2, E.2 Salt bridges: A:R.167, A:H.510, A:K.656 GLU.14: 14 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.18, GOL.22, MPO.24 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.14, E.14 Water bridges: B:E.382, E.14, E.14 Salt bridges: B:R.167, B:H.510, B:K.656

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

NAG.3: 4 residues within 4Å: Chain A: N.78, T.80, N.81, I.306 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.306 Hydrogen bonds: A:N.78, A:T.80, A:N.81 Water bridges: A:Q.124 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.5: 2 residues within 4Å: Chain A: N.152, T.154 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.154 NAG.15: 4 residues within 4Å: Chain B: N.78, T.80, N.81, I.306 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.306 Hydrogen bonds: B:N.78, B:N.81 Water bridges: B:Q.124 NAG.16: 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 NAG.17: 2 residues within 4Å: Chain B: N.152, T.154 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.154

4 x ZN: ZINC ION(Non-covalent)

ZN.6: 7 residues within 4Å: Chain A: D.344, E.382, Y.509, H.510 Ligands: GLU.2, ZN.7, MPO.12 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.344, A:E.382, A:H.510, H2O.4, H2O.4 ZN.7: 5 residues within 4Å: Chain A: H.334, D.344, D.410 Ligands: ZN.6, MPO.12 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.4 ZN.18: 7 residues within 4Å: Chain B: D.344, E.382, Y.509, H.510 Ligands: GLU.14, ZN.19, MPO.24 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.344, B:E.382, B:H.510, H2O.32, H2O.32 ZN.19: 5 residues within 4Å: Chain B: H.334, D.344, D.410 Ligands: ZN.18, MPO.24 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.32

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

CL.8: 5 residues within 4Å: Chain A: N.408, D.410, R.491, R.493, R.537 Ligand excluded by PLIP CL.20: 5 residues within 4Å: Chain B: N.408, D.410, R.491, R.493, R.537 Ligand excluded by PLIP

2 x CA: CALCIUM ION(Non-covalent)

CA.9: 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.21: 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

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 6 residues within 4Å: Chain A: F.166, R.167, Y.509, N.655, Y.657 Ligands: GLU.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:R.167, A:Y.509, A:Y.657, E.2, E.2 GOL.11: 7 residues within 4Å: Chain A: L.636, G.637, L.638, P.639, K.687, H.688, I.691 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:L.638 Water bridges: A:G.640, A:K.641, A:K.687, A:K.687, A:K.687, A:K.687 GOL.22: 6 residues within 4Å: Chain B: F.166, R.167, Y.509, N.655, Y.657 Ligands: GLU.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.167, B:Y.509 GOL.23: 7 residues within 4Å: Chain B: L.636, G.637, L.638, P.639, K.687, H.688, I.691 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.638 Water bridges: B:G.640, B:K.641, B:K.687, B:K.687, B:K.687, B:K.687, A:Y.229

2 x MPO: 3[N-MORPHOLINO]PROPANE SULFONIC ACID(Non-covalent)

MPO.12: 17 residues within 4Å: Chain A: F.166, R.167, N.214, H.334, D.344, E.381, E.382, G.384, L.385, D.410, G.475, Y.509, H.510, K.656 Ligands: GLU.2, ZN.6, ZN.7 11 PLIP interactions: 7 interactions with chain A, 4 Ligand-Ligand interactions Hydrogen bonds: A:N.214, A:K.656, E.2, E.2 Water bridges: A:R.167 Salt bridges: A:H.334, A:E.381, A:E.382, A:H.510, E.2 Hydrophobic interactions: E.2 MPO.24: 17 residues within 4Å: Chain B: F.166, R.167, N.214, H.334, D.344, E.381, E.382, G.384, L.385, D.410, G.475, Y.509, H.510, K.656 Ligands: GLU.14, ZN.18, ZN.19 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.214, B:Y.509, B:K.656 Water bridges: B:R.167 Salt bridges: B:H.334, B:E.381, B:E.382, 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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