SMTL ID : 2c6c.1

membrane-bound glutamate carboxypeptidase II (GCPII) in complex with GPI-18431 (S)-2-(4-iodobenzylphosphonomethyl)-pentanedioic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

4 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 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.433, P.551 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain B: N.33, Q.52 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain B: N.433, P.551 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN-MAN.3: 8 residues within 4Å: Chain A: S.588, S.591, 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:R.311 NAG-NAG-MAN-MAN.15: 8 residues within 4Å: Chain A: H.69, E.233, Y.234, R.311 Chain B: S.588, S.591, N.595, Q.697 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.311

4 x ZN: ZINC ION(Non-covalent)

ZN.4: 6 residues within 4Å: Chain A: D.344, E.382, Y.509, H.510 Ligands: ZN.5, 24I.12 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.344, A:E.382, A:E.382, A:H.510 ZN.5: 7 residues within 4Å: Chain A: H.334, D.344, E.381, E.382, D.410 Ligands: ZN.4, 24I.12 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.334, A:D.344, A:D.410, A:D.410 ZN.16: 6 residues within 4Å: Chain B: D.344, E.382, Y.509, H.510 Ligands: ZN.17, 24I.24 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.344, B:E.382, B:E.382, B:H.510 ZN.17: 7 residues within 4Å: Chain B: H.334, D.344, E.381, E.382, D.410 Ligands: ZN.16, 24I.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.6: 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.2 CA.18: 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.9

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.19: 4 residues within 4Å: Chain B: N.408, D.410, R.491, R.537 Ligand excluded by PLIP

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

NAG.8: 4 residues within 4Å: Chain A: N.78, T.80, H.81, T.306 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.306 Hydrogen bonds: A:T.80, A:H.81 NAG.9: 4 residues within 4Å: Chain A: Y.84, E.94, I.95, N.97 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.84, A:E.94, A:E.94, A:N.97 NAG.10: 2 residues within 4Å: Chain A: N.152, S.154 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.152 NAG.11: 4 residues within 4Å: Chain A: W.203, N.416, F.522, Y.523 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.203, A:Y.523 Hydrogen bonds: A:F.522 NAG.20: 4 residues within 4Å: Chain B: N.78, T.80, H.81, T.306 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.306 Hydrogen bonds: B:T.80, B:H.81 NAG.21: 4 residues within 4Å: Chain B: Y.84, E.94, I.95, N.97 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.84, B:E.94, B:E.94, B:N.97 NAG.22: 2 residues within 4Å: Chain B: N.152, S.154 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.152 NAG.23: 4 residues within 4Å: Chain B: W.203, N.416, F.522, Y.523 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.203, B:Y.523 Hydrogen bonds: B:F.522

2 x 24I: (2S)-2-{[HYDROXY(4-IODOBENZYL)PHOSPHORYL]METHYL}PENTANEDIOIC ACID(Non-covalent)

24I.12: 22 residues within 4Å: Chain A: R.167, N.214, H.334, D.344, E.381, E.382, G.384, L.385, D.410, S.411, I.413, E.414, G.475, N.476, R.493, Y.506, Y.509, H.510, K.656, Y.657 Ligands: ZN.4, ZN.5 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.509 Hydrogen bonds: A:N.214, A:N.214, A:G.475, A:N.476, A:Y.509 Water bridges: A:K.656 Salt bridges: A:R.167, A:H.510, A:K.656 Halogen bonds: A:I.413 24I.24: 22 residues within 4Å: Chain B: R.167, N.214, H.334, D.344, E.381, E.382, G.384, L.385, D.410, S.411, I.413, E.414, G.475, N.476, R.493, Y.506, Y.509, H.510, K.656, Y.657 Ligands: ZN.16, ZN.17 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Y.509 Hydrogen bonds: B:N.214, B:N.214, B:E.382, B:G.475, B:N.476, B:Y.509 Water bridges: B:K.656 Salt bridges: B:R.167, B:H.510, B:K.656 Halogen bonds: B:I.413

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mesters, J.R. et al., Structure of Glutamate Carboxypeptidase II, a Drug Target in Neuronal Damage and Prostate Cancer. Embo J. (2006)

Release Date

2006-02-15

Peptides

GLUTAMATE CARBOXYPEPTIDASE II: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

GLUTAMATE CARBOXYPEPTIDASE II

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