SMTL ID : 2jbj.1

membrane-bound glutamate carboxypeptidase II (GCPII) in complex with 2-PMPA (2-phosphonoMethyl-pentanedioic acid)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

homo-dimer

Ligands

6 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: 2 residues within 4Å: Chain A: N.33, Q.52 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.52 Water bridges: 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 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.555 NAG-NAG.13: 2 residues within 4Å: Chain B: N.33, Q.52 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Q.52 Water bridges: B:S.55 NAG-NAG.14: 4 residues within 4Å: Chain B: Y.84, E.94, I.95, N.97 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain B: S.429, L.430, N.433, P.551 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.555

2 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(Non-functional Binders)

NAG-NAG-BMA-MAN.4: 9 residues within 4Å: Chain A: S.588, S.591, A.592, N.595, Q.697 Chain B: H.69, E.233, Y.234, R.311 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.233, B:R.311, B:R.311, B:R.311 NAG-NAG-BMA-MAN.16: 9 residues within 4Å: Chain A: H.69, E.233, Y.234, R.311 Chain B: S.588, S.591, A.592, N.595, Q.697 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.233, A:R.311, A:R.311, A:R.311

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, G88.12 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.344, A:E.382, A:E.382, A:H.510 ZN.6: 7 residues within 4Å: Chain A: H.334, D.344, E.381, E.382, D.410 Ligands: ZN.5, G88.12 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.334, A:D.344, A:D.410, A:D.410 ZN.17: 6 residues within 4Å: Chain B: D.344, E.382, Y.509, H.510 Ligands: ZN.18, G88.24 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.344, B:E.382, B:E.382, B:H.510 ZN.18: 7 residues within 4Å: Chain B: H.334, D.344, E.381, E.382, D.410 Ligands: ZN.17, G88.24 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.334, B:D.344, B:D.410, B:D.410

2 x CA: CALCIUM ION(Non-covalent)

CA.7: 4 residues within 4Å: Chain A: T.226, Y.229, E.390, E.393 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.226, A:E.390, A:E.390, A:E.393, H2O.5 CA.19: 4 residues within 4Å: Chain B: T.226, Y.229, E.390, E.393 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.226, B:E.390, B:E.390, B:E.393, H2O.21

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

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

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

NAG.9: 4 residues within 4Å: Chain A: N.78, T.80, H.81, T.306 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.80, A:T.306 NAG.10: 2 residues within 4Å: Chain A: N.152, S.154 No protein-ligand interaction detected (PLIP) NAG.11: 4 residues within 4Å: Chain A: W.203, N.416, F.522, Y.523 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.203, A:Y.523 Hydrogen bonds: A:W.203, A:F.522 NAG.21: 4 residues within 4Å: Chain B: N.78, T.80, H.81, T.306 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.80, B:T.306 NAG.22: 2 residues within 4Å: Chain B: N.152, S.154 No protein-ligand interaction detected (PLIP) NAG.23: 4 residues within 4Å: Chain B: W.203, N.416, F.522, Y.523 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.203, B:Y.523 Hydrogen bonds: B:W.203, B:F.522

2 x G88: (2S)-2-(PHOSPHONOMETHYL)PENTANEDIOIC ACID(Non-covalent)

G88.12: 17 residues within 4Å: Chain A: R.167, N.214, H.334, D.344, E.381, E.382, G.384, L.385, D.410, G.475, N.476, Y.509, H.510, K.656, Y.657 Ligands: ZN.5, ZN.6 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.214, A:N.214, A:G.475, A:N.476, A:Y.509 Water bridges: A:N.214, A:K.656 Salt bridges: A:R.167, A:H.510, A:K.656 G88.24: 17 residues within 4Å: Chain B: R.167, N.214, H.334, D.344, E.381, E.382, G.384, L.385, D.410, G.475, N.476, Y.509, H.510, K.656, Y.657 Ligands: ZN.17, ZN.18 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:N.214, B:N.214, B:E.382, B:G.475, B:N.476, B:Y.509 Water bridges: B:N.214, B:K.656 Salt bridges: B:R.167, B:H.510, B:K.656

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mesters, J.R. et al., Human Glutamate Carboxypeptidase II Inhibition: Structures of Gcpii in Complex with Two Potent Inhibitors, Quisqualate and 2-Pmpa. Acta Crystallogr.,Sect.D (2007)

Release Date

2006-12-18

Peptides

GLUTAMATE CARBOXYPEPTIDASE 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

GLUTAMATE CARBOXYPEPTIDASE 2

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