SMTL ID : 4w9y.1

X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a glutamyl sulfamide inhibitor CJC47

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.64 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.33, Q.36, Q.52, S.55, Q.56 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.52 NAG-NAG.2: 5 residues within 4Å: Chain A: Y.84, E.94, I.95, F.96, N.97 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain A: S.429, L.430, N.433, P.551, R.555, Q.608 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 5 residues within 4Å: Chain B: N.33, Q.36, Q.52, S.55, Q.56 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Q.52 NAG-NAG.14: 5 residues within 4Å: Chain B: Y.84, E.94, I.95, F.96, N.97 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 6 residues within 4Å: Chain B: S.429, L.430, N.433, P.551, R.555, Q.608 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

NAG-NAG-BMA-MAN.4: 10 residues within 4Å: Chain A: S.588, S.591, A.592, N.595, A.693, Q.697 Chain B: H.69, E.233, Y.234, R.311 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.69, B:E.233, B:R.311, B:R.311 Water bridges: B:R.311 NAG-NAG-BMA-MAN.16: 10 residues within 4Å: Chain A: H.69, E.233, Y.234, R.311 Chain B: S.588, S.591, A.592, N.595, A.693, Q.697 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.69, A:E.233, A:R.311, A:R.311 Water bridges: A:R.311

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

NAG.5: 5 residues within 4Å: Chain A: N.78, T.80, H.81, Q.124, T.306 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.306 NAG.6: 2 residues within 4Å: Chain A: N.152, S.154 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.154 NAG.7: 5 residues within 4Å: Chain A: W.203, G.415, N.416, F.522, Y.523 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.203, A:Y.523 Hydrogen bonds: A:W.203, A:F.522 Water bridges: A:N.416 NAG.17: 5 residues within 4Å: Chain B: N.78, T.80, H.81, Q.124, T.306 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.306 NAG.18: 2 residues within 4Å: Chain B: N.152, S.154 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.154 NAG.19: 5 residues within 4Å: Chain B: W.203, G.415, N.416, F.522, Y.523 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.203, B:Y.523 Hydrogen bonds: B:W.203, B:F.522 Water bridges: B:N.416

4 x ZN: ZINC ION(Non-covalent)

ZN.8: 8 residues within 4Å: Chain A: H.334, W.338, D.344, E.382, Y.509, H.510 Ligands: ZN.9, 3K0.12 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.344, A:E.382, A:E.382, A:H.510 ZN.9: 9 residues within 4Å: Chain A: H.334, D.344, P.345, E.381, E.382, D.410, N.476 Ligands: ZN.8, 3K0.12 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.334, A:D.344, A:D.410, A:D.410, H2O.7 ZN.20: 8 residues within 4Å: Chain B: H.334, W.338, D.344, E.382, Y.509, H.510 Ligands: ZN.21, 3K0.24 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.344, B:E.382, B:E.382, B:H.510 ZN.21: 9 residues within 4Å: Chain B: H.334, D.344, P.345, E.381, E.382, D.410, N.476 Ligands: ZN.20, 3K0.24 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.334, B:D.344, B:D.410, B:D.410, H2O.29

2 x CA: CALCIUM ION(Non-covalent)

CA.10: 8 residues within 4Å: Chain A: D.223, T.226, P.227, Y.229, P.230, A.231, E.390, E.393 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:T.226, A:Y.229, A:E.390, A:E.390, A:E.393 CA.22: 8 residues within 4Å: Chain B: D.223, T.226, P.227, Y.229, P.230, A.231, E.390, E.393 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:T.226, B:Y.229, B:E.390, B:E.390, B:E.393

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

CL.11: 5 residues within 4Å: Chain A: N.408, D.410, R.491, R.493, R.537 Ligand excluded by PLIP CL.23: 5 residues within 4Å: Chain B: N.408, D.410, R.491, R.493, R.537 Ligand excluded by PLIP

2 x 3K0: N-sulfamoyl-L-glutamic acid(Non-covalent)

3K0.12: 18 residues within 4Å: Chain A: F.166, 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.8, ZN.9 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.385 Hydrogen bonds: A:N.214, A:E.381, A:G.475, A:N.476, A:Y.509, A:Y.657 Water bridges: A:S.411, A:K.656, A:K.656 Salt bridges: A:R.167, A:H.510, A:K.656 3K0.24: 18 residues within 4Å: Chain B: F.166, 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.20, ZN.21 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:L.385 Hydrogen bonds: B:N.214, B:D.344, B:E.381, B:G.475, B:N.476, B:Y.509, B:Y.657 Water bridges: B:S.411, B:K.656, B:K.656 Salt bridges: B:R.167, B:H.510, B:K.656

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Novakova, Z. et al., Structural, Biochemical, and Computational Characterization of Sulfamides as Bimetallic Peptidase Inhibitors. J.Chem.Inf.Model. (2024)

Release Date

2015-09-23

Peptides

Glutamate carboxypeptidase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glutamate carboxypeptidase 2

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