SMTL ID : 2xef.1

Human glutamate carboxypeptidase II in complex with Antibody- Recruiting Molecule ARM-P8

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.59 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: 5 residues within 4Å: Chain A: N.35, Q.38, Q.54, S.57, Q.58 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.54 NAG-NAG.2: 4 residues within 4Å: Chain A: Y.86, E.96, I.97, N.99 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: S.431, L.432, N.435, P.553, Q.610 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 5 residues within 4Å: Chain B: N.35, Q.38, Q.54, S.57, Q.58 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Q.54 NAG-NAG.14: 4 residues within 4Å: Chain B: Y.86, E.96, I.97, N.99 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 5 residues within 4Å: Chain B: S.431, L.432, N.435, P.553, Q.610 No protein-ligand interaction detected (PLIP)

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-covalent)

NAG-NAG-BMA-MAN.4: 9 residues within 4Å: Chain A: S.590, S.593, A.594, N.597, Q.699 Chain B: H.71, E.235, Y.236, R.313 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.235, B:E.235, B:R.313, B:R.313 Water bridges: B:E.235 NAG-NAG-BMA-MAN.16: 9 residues within 4Å: Chain A: H.71, E.235, Y.236, R.313 Chain B: S.590, S.593, A.594, N.597, Q.699 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.235, A:E.235, A:R.313, A:R.313 Water bridges: A:E.235

2 x AR8: N-{[(1S)-5-{4-[25-({2,4-BIS[HYDROXY(OXO)AMMONIO]PHENYL}AMINO)-2,5,8,11,14,17,20,23-OCTAOXAPENTACOS-1-YL]-1H-1,2,3-TRIAZOL-1-YL}-1-CARBOXYPENTYL]CARBAMOYL}-L-GLUTAMIC ACID(Non-covalent)

AR8.5: 31 residues within 4Å: Chain A: K.166, R.169, N.216, D.346, E.383, E.384, G.386, L.387, R.422, D.424, S.460, R.470, S.472, K.473, L.474, G.475, G.477, N.478, R.493, R.495, T.497, W.500, E.501, Y.511, H.512, N.657, K.658, Y.659, A.660, G.661 Ligands: ZN.6 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:W.500, A:Y.511, A:Y.659, A:Y.659 Hydrogen bonds: A:N.216, A:S.472, A:G.475, A:G.477, A:G.477, A:N.478, A:Y.511, A:N.657, A:G.661 Water bridges: A:N.216, A:D.346, A:R.422, A:R.422, A:S.472, A:K.473, A:R.493 Salt bridges: A:R.169, A:R.493, A:R.495, A:H.512, A:K.658 pi-Stacking: A:W.500 pi-Cation interactions: A:R.470 AR8.17: 31 residues within 4Å: Chain B: K.166, R.169, N.216, D.346, E.383, E.384, G.386, L.387, R.422, D.424, S.460, R.470, S.472, K.473, L.474, G.475, G.477, N.478, R.493, R.495, T.497, W.500, E.501, Y.511, H.512, N.657, K.658, Y.659, A.660, G.661 Ligands: ZN.18 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:W.500, B:Y.511, B:Y.659, B:Y.659 Hydrogen bonds: B:N.216, B:S.472, B:G.475, B:G.477, B:G.477, B:N.478, B:Y.511, B:N.657, B:G.661 Water bridges: B:N.216, B:D.346, B:R.422, B:R.422, B:S.472, B:K.473, B:R.493 Salt bridges: B:R.169, B:R.493, B:R.495, B:H.512, B:K.658 pi-Stacking: B:W.500 pi-Cation interactions: B:R.470

4 x ZN: ZINC ION(Non-covalent)

ZN.6: 5 residues within 4Å: Chain A: D.346, E.384, H.512 Ligands: AR8.5, ZN.7 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.346, A:E.384, A:E.384, A:H.512, H2O.22 ZN.7: 6 residues within 4Å: Chain A: H.336, D.346, E.383, E.384, D.412 Ligands: ZN.6 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.336, A:D.346, A:D.412, A:D.412, H2O.22 ZN.18: 5 residues within 4Å: Chain B: D.346, E.384, H.512 Ligands: AR8.17, ZN.19 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.346, B:E.384, B:E.384, B:H.512, H2O.44 ZN.19: 6 residues within 4Å: Chain B: H.336, D.346, E.383, E.384, D.412 Ligands: ZN.18 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.336, B:D.346, B:D.412, B:D.412, H2O.44

2 x CA: CALCIUM ION(Non-covalent)

CA.8: 4 residues within 4Å: Chain A: T.228, Y.231, E.392, E.395 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:T.228, A:Y.231, A:E.392, A:E.392, A:E.395 CA.20: 4 residues within 4Å: Chain B: T.228, Y.231, E.392, E.395 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:T.228, B:Y.231, B:E.392, B:E.392, B:E.395

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

CL.9: 4 residues within 4Å: Chain A: N.410, D.412, R.493, R.495 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain B: N.410, D.412, R.493, R.495 Ligand excluded by PLIP

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

NAG.10: 4 residues within 4Å: Chain A: N.80, T.82, H.83, T.308 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.80, A:T.82 Water bridges: A:Q.126 NAG.11: 2 residues within 4Å: Chain A: N.154, S.156 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.156 NAG.12: 4 residues within 4Å: Chain A: W.205, N.418, F.524, Y.525 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.205, A:Y.525 Hydrogen bonds: A:W.205, A:F.524 Water bridges: A:N.418 NAG.22: 4 residues within 4Å: Chain B: N.80, T.82, H.83, T.308 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.80, B:T.82 Water bridges: B:Q.126 NAG.23: 2 residues within 4Å: Chain B: N.154, S.156 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.156 NAG.24: 4 residues within 4Å: Chain B: W.205, N.418, F.524, Y.525 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.205, B:Y.525 Hydrogen bonds: B:W.205, B:F.524 Water bridges: B:N.418

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, A.X. et al., A Remote Arene-Binding Site on Prostate Specific Membrane Antigen Revealed by Antibody-Recruiting Small Molecules. J.Am.Chem.Soc. (2010)

Release Date

2010-09-08

Peptides

GLUTAMATE CARBOXYPEPTIDASE 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

GLUTAMATE CARBOXYPEPTIDASE 2

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