SMTL ID : 6fe5.1

X-ray structure of human glutamate carboxypeptidase II (GCPII) - the E424M inactive mutant, in complex with a inhibitor JHU 2249

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.52 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.33, Q.36, Q.52, S.55, Q.56 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: Y.84, E.94, I.95, N.97 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 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain B: Y.84, E.94, I.95, N.97 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.3: 6 residues within 4Å: Chain A: S.429, L.430, N.433, P.551, Q.608, D.609 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.609, A:Q.608 NAG-NAG-BMA-MAN.15: 6 residues within 4Å: Chain B: S.429, L.430, N.433, P.551, Q.608, D.609 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.609, B:Q.608

2 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN.4: 10 residues within 4Å: Chain A: S.588, S.591, A.592, N.595, Q.697 Chain B: L.67, H.69, E.233, Y.234, R.311 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.233, B:R.311, B:R.311, B:L.67, B:H.69 Water bridges: B:H.69 NAG-NAG-BMA-MAN-MAN.16: 10 residues within 4Å: Chain A: L.67, H.69, E.233, Y.234, R.311 Chain B: S.588, S.591, A.592, N.595, Q.697 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.233, A:R.311, A:R.311, A:L.67, A:H.69 Water bridges: A:H.69

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

NAG.5: 4 residues within 4Å: Chain A: N.78, T.80, H.81, T.306 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.78, A:T.80 Water bridges: A:Q.124 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.11: 4 residues within 4Å: Chain A: W.203, 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: 4 residues within 4Å: Chain B: N.78, T.80, H.81, T.306 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.78, B:T.80 Water bridges: B:Q.124 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.23: 4 residues within 4Å: Chain B: W.203, 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.7: 5 residues within 4Å: Chain A: D.344, E.382, H.510 Ligands: ZN.8, D6E.12 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.344, A:E.382, A:E.382, A:H.510, H2O.16 ZN.8: 6 residues within 4Å: Chain A: H.334, D.344, M.381, E.382, D.410 Ligands: ZN.7 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.16 ZN.19: 5 residues within 4Å: Chain B: D.344, E.382, H.510 Ligands: ZN.20, D6E.24 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.344, B:E.382, B:E.382, B:H.510, H2O.38 ZN.20: 6 residues within 4Å: Chain B: H.334, D.344, M.381, E.382, D.410 Ligands: ZN.19 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.38

2 x CA: CALCIUM ION(Non-covalent)

CA.9: 4 residues within 4Å: Chain A: T.226, Y.229, 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.21: 4 residues within 4Å: Chain B: T.226, Y.229, 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.10: 4 residues within 4Å: Chain A: N.408, D.410, R.491, R.493 Ligand excluded by PLIP CL.22: 4 residues within 4Å: Chain B: N.408, D.410, R.491, R.493 Ligand excluded by PLIP

2 x D6E: (2~{S})-2-[[(2~{S})-4-methyl-1-oxidanyl-1-oxidanylidene-pentan-2-yl]carbamoylamino]pentanedioic acid(Non-covalent)

D6E.12: 19 residues within 4Å: Chain A: F.166, R.167, N.214, D.344, M.381, E.382, G.384, L.385, G.475, N.476, R.491, R.493, K.502, F.503, Y.509, H.510, K.656, Y.657 Ligands: ZN.7 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.509, A:Y.657 Hydrogen bonds: A:N.214, A:G.475, A:G.475, A:N.476 Water bridges: A:N.214, A:R.491 Salt bridges: A:R.167, A:R.491, A:R.493, A:H.510, A:K.656 D6E.24: 19 residues within 4Å: Chain B: F.166, R.167, N.214, D.344, M.381, E.382, G.384, L.385, G.475, N.476, R.491, R.493, K.502, F.503, Y.509, H.510, K.656, Y.657 Ligands: ZN.19 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.509, B:Y.657 Hydrogen bonds: B:N.214, B:G.475, B:G.475, B:N.476 Water bridges: B:N.214, B:R.491 Salt bridges: B:R.167, B:R.491, B:R.493, B:H.510, B:K.656

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Barinka, C. et al., Structural and computational basis for potent inhibition of glutamate carboxypeptidase II by carbamate-based inhibitors. Bioorg.Med.Chem. (2019)

Release Date

2019-01-30

Peptides

Glutamate carboxypeptidase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glutamate carboxypeptidase 2

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