SMTL ID : 2xeg.1

Human glutamate carboxypeptidase II in complex with Antibody- Recruiting Molecule ARM-P4

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: 4 residues within 4Å: Chain A: N.35, Q.38, Q.54, Q.58 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.54 NAG-NAG.2: 5 residues within 4Å: Chain A: Y.86, E.96, I.97, F.98, 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.610 NAG-NAG.13: 4 residues within 4Å: Chain B: N.35, Q.38, Q.54, Q.58 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Q.54 NAG-NAG.14: 5 residues within 4Å: Chain B: Y.86, E.96, I.97, F.98, 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 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.610

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.590, S.593, A.594, N.597, Q.699 Chain B: H.71, E.235, Y.236, R.313 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.235, B:E.235, B:R.313, B:R.313 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.235, A:E.235, A:R.313, A:R.313

4 x ZN: ZINC ION(Non-covalent)

ZN.5: 5 residues within 4Å: Chain A: D.346, E.384, H.512 Ligands: ZN.6, CI9.12 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.346, A:E.384, A:E.384, A:H.512 ZN.6: 6 residues within 4Å: Chain A: H.336, D.346, E.383, E.384, D.412 Ligands: ZN.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.336, A:D.346, A:D.412, A:D.412 ZN.17: 5 residues within 4Å: Chain B: D.346, E.384, H.512 Ligands: ZN.18, CI9.24 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.346, B:E.384, B:E.384, B:H.512 ZN.18: 6 residues within 4Å: Chain B: H.336, D.346, E.383, E.384, D.412 Ligands: ZN.17 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.336, B:D.346, B:D.412, B:D.412

2 x CA: CALCIUM ION(Non-covalent)

CA.7: 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.19: 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.8: 4 residues within 4Å: Chain A: N.410, D.412, R.493, R.495 Ligand excluded by PLIP CL.20: 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.9: 4 residues within 4Å: Chain A: N.80, T.82, H.83, T.308 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.308 Hydrogen bonds: A:N.80, A:T.82 NAG.10: 2 residues within 4Å: Chain A: N.154, S.156 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.156 NAG.11: 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.21: 4 residues within 4Å: Chain B: N.80, T.82, H.83, T.308 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.308 Hydrogen bonds: B:N.80, B:T.82 NAG.22: 2 residues within 4Å: Chain B: N.154, S.156 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.156 NAG.23: 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

2 x CI9: N-({(1S)-5-[4-(13-{[2,4-BIS(DIHYDROXYAMINO)PHENYL]AMINO}-2,5,8,11-TETRAOXATRIDEC-1-YL)-1H-1,2,3-TRIAZOL-1-YL]-1-CARBOXYPENTYL}CARBAMOYL)-L-GLUTAMIC ACID(Non-covalent)

CI9.12: 27 residues within 4Å: Chain A: K.166, V.167, F.168, R.169, N.216, D.346, E.383, E.384, G.386, L.387, R.422, S.460, R.470, S.472, G.477, N.478, R.493, R.495, W.500, E.501, Y.511, H.512, N.657, K.658, Y.659, A.660 Ligands: ZN.5 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:W.500, A:Y.511, A:Y.659, A:Y.659 Hydrogen bonds: A:N.216, A:E.384, A:S.472, A:S.472, A:G.477, A:G.477, A:G.477, A:N.478 Water bridges: A:Q.213, A:N.216, A:R.493, A:K.658 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 CI9.24: 27 residues within 4Å: Chain B: K.166, V.167, F.168, R.169, N.216, D.346, E.383, E.384, G.386, L.387, R.422, S.460, R.470, S.472, G.477, N.478, R.493, R.495, W.500, E.501, Y.511, H.512, N.657, K.658, Y.659, A.660 Ligands: ZN.17 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:W.500, B:Y.511, B:Y.659, B:Y.659 Hydrogen bonds: B:N.216, B:E.384, B:S.472, B:S.472, B:G.477, B:G.477, B:G.477, B:N.478 Water bridges: B:Q.213, B:N.216, B:R.493, B:K.658 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

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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