SMTL ID : 3sjx.1

X-ray structure of human glutamate carboxypeptidase II (the E424A inactive mutant) in complex with N-acetyl-aspartyl-methionine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.66 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: 5 residues within 4Å: Chain A: N.35, Q.38, Q.54, S.57, Q.58 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.54 Hydrogen bonds: A:S.57 NAG-NAG.2: 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.12: 5 residues within 4Å: Chain B: N.35, Q.38, Q.54, S.57, Q.58 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Q.54 Hydrogen bonds: B:S.57 NAG-NAG.13: 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-covalent)

NAG-NAG-BMA-MAN.3: 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:R.313, B:R.313 NAG-NAG-BMA-MAN.14: 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:R.313, A:R.313

4 x ZN: ZINC ION(Non-covalent)

ZN.4: 5 residues within 4Å: Chain A: D.346, E.384, H.512 Ligands: ZN.5, QRG.11 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.16 ZN.5: 6 residues within 4Å: Chain A: H.336, D.346, E.384, D.412 Ligands: ZN.4, QRG.11 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.16 ZN.15: 5 residues within 4Å: Chain B: D.346, E.384, H.512 Ligands: ZN.16, QRG.22 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.34 ZN.16: 6 residues within 4Å: Chain B: H.336, D.346, E.384, D.412 Ligands: ZN.15, QRG.22 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.34

2 x CA: CALCIUM ION(Non-covalent)

CA.6: 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.17: 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.7: 5 residues within 4Å: Chain A: N.410, D.412, R.493, R.495, R.539 Ligand excluded by PLIP CL.18: 5 residues within 4Å: Chain B: N.410, D.412, R.493, R.495, R.539 Ligand excluded by PLIP

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

NAG.8: 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:T.82 Water bridges: A:N.80 NAG.9: 2 residues within 4Å: Chain A: N.154, S.156 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.154 NAG.10: 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.19: 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:T.82 Water bridges: B:N.80 NAG.20: 2 residues within 4Å: Chain B: N.154, S.156 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:N.154 NAG.21: 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 QRG: N-acetyl-L-alpha-aspartyl-L-methionine(Non-covalent)

QRG.11: 19 residues within 4Å: Chain A: F.168, R.169, N.216, D.346, A.383, E.384, G.386, D.412, S.413, G.477, N.478, R.493, R.495, Y.511, H.512, K.658, Y.659 Ligands: ZN.4, ZN.5 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:D.346, A:Y.659 Hydrogen bonds: A:D.346, A:G.477, A:G.477, A:N.478, A:R.493, A:R.495, A:R.495, A:Y.511 Water bridges: A:N.216, A:R.422, A:R.493 Salt bridges: A:R.169, A:R.493, A:R.495, A:H.512 QRG.22: 19 residues within 4Å: Chain B: F.168, R.169, N.216, D.346, A.383, E.384, G.386, D.412, S.413, G.477, N.478, R.493, R.495, Y.511, H.512, K.658, Y.659 Ligands: ZN.15, ZN.16 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:D.346, B:Y.659 Hydrogen bonds: B:D.346, B:G.477, B:G.477, B:N.478, B:R.493, B:R.495, B:R.495, B:Y.511 Water bridges: B:N.216, B:R.422, B:R.493 Salt bridges: B:R.169, B:R.493, B:R.495, B:H.512

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Plechanovova, A. et al., Novel Substrate-Based Inhibitors of Human Glutamate Carboxypeptidase II with Enhanced Lipophilicity. J.Med.Chem. (2011)

Release Date

2011-10-05

Peptides

Glutamate carboxypeptidase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glutamate carboxypeptidase 2

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