SMTL ID : 4mcs.1

A high resolution structure of human glutamate carboxypeptidase II (GCPII) His475Tyr variant in complex with glutamic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.83 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: 6 residues within 4Å: Chain A: N.83, Q.86, Q.102, S.105, Q.106, E.109 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.105 NAG-NAG.2: 5 residues within 4Å: Chain A: Y.134, E.144, I.145, F.146, N.147 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: S.479, L.480, N.483, P.601, Q.658 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.658 NAG-NAG.14: 6 residues within 4Å: Chain B: N.83, Q.86, Q.102, S.105, Q.106, E.109 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.105 NAG-NAG.15: 5 residues within 4Å: Chain B: Y.134, E.144, I.145, F.146, N.147 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 5 residues within 4Å: Chain B: S.479, L.480, N.483, P.601, Q.658 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.658

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(Post Translational Modification)

NAG-NAG-BMA-MAN.4: 9 residues within 4Å: Chain A: S.638, S.641, A.642, N.645, Q.747 Chain B: H.119, E.283, Y.284, R.361 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.283, B:R.361, B:R.361 Water bridges: B:H.119, B:R.361 NAG-NAG-BMA-MAN.17: 9 residues within 4Å: Chain A: H.119, E.283, Y.284, R.361 Chain B: S.638, S.641, A.642, N.645, Q.747 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.283, A:R.361, A:R.361 Water bridges: A:H.119, A:R.361

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

NAG.5: 4 residues within 4Å: Chain A: N.128, T.130, H.131, T.356 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.356 Hydrogen bonds: A:T.130 Water bridges: A:N.128 NAG.6: 2 residues within 4Å: Chain A: N.202, S.204 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.204 NAG.7: 4 residues within 4Å: Chain A: W.253, N.466, F.572, Y.573 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.253, A:Y.573 Hydrogen bonds: A:W.253, A:F.572 Water bridges: A:N.466 NAG.18: 4 residues within 4Å: Chain B: N.128, T.130, H.131, T.356 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.356 Hydrogen bonds: B:T.130 Water bridges: B:N.128 NAG.19: 2 residues within 4Å: Chain B: N.202, S.204 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.204 NAG.20: 4 residues within 4Å: Chain B: W.253, N.466, F.572, Y.573 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.253, B:Y.573 Hydrogen bonds: B:W.253, B:F.572 Water bridges: B:N.466

4 x ZN: ZINC ION(Non-covalent)

ZN.8: 5 residues within 4Å: Chain A: D.394, E.432, H.560 Ligands: ZN.9, ASP.13 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: A:D.394, A:E.432, A:H.560, ASP.13, H2O.22 ZN.9: 7 residues within 4Å: Chain A: H.384, D.394, E.431, E.432, D.460 Ligands: ZN.8, ASP.13 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.384, A:D.394, A:D.460, A:D.460, H2O.22 ZN.21: 5 residues within 4Å: Chain B: D.394, E.432, H.560 Ligands: ZN.22, ASP.26 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.394, B:E.432, B:E.432, B:H.560, H2O.44 ZN.22: 7 residues within 4Å: Chain B: H.384, D.394, E.431, E.432, D.460 Ligands: ZN.21, ASP.26 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.384, B:D.394, B:D.460, B:D.460, H2O.44

2 x CA: CALCIUM ION(Non-covalent)

CA.10: 4 residues within 4Å: Chain A: T.276, Y.279, E.440, E.443 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.276, A:Y.279, A:E.440, A:E.443, H2O.1 CA.23: 4 residues within 4Å: Chain B: T.276, Y.279, E.440, E.443 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.276, B:Y.279, B:E.440, B:E.443, H2O.23

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

CL.11: 4 residues within 4Å: Chain A: N.458, D.460, R.541, R.587 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain B: N.458, D.460, R.541, R.587 Ligand excluded by PLIP

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.12: 12 residues within 4Å: Chain A: R.217, N.264, E.431, E.432, G.434, L.435, G.525, Y.559, H.560, K.706, Y.707 Ligands: ASP.13 9 PLIP interactions: 1 Ligand-Ligand interactions, 8 interactions with chain A Hydrogen bonds: D.13, A:N.264, A:E.431, A:E.432, A:Y.559 Hydrophobic interactions: A:L.435 Salt bridges: A:R.217, A:H.560, A:K.706 GLU.25: 12 residues within 4Å: Chain B: R.217, N.264, E.431, E.432, G.434, L.435, G.525, Y.559, H.560, K.706, Y.707 Ligands: ASP.26 9 PLIP interactions: 1 Ligand-Ligand interactions, 8 interactions with chain B Hydrogen bonds: D.26, B:N.264, B:E.431, B:E.432, B:Y.559 Hydrophobic interactions: B:L.435 Salt bridges: B:R.217, B:H.560, B:K.706

2 x ASP: ASPARTIC ACID(Non-covalent)

ASP.13: 11 residues within 4Å: Chain A: D.394, D.460, G.525, N.526, R.541, Y.559, H.560, Y.707 Ligands: ZN.8, ZN.9, GLU.12 11 PLIP interactions: 5 Ligand-Ligand interactions, 6 interactions with chain A Hydrogen bonds: E.12, D.13, D.13, D.13, D.13, A:N.526 Hydrophobic interactions: A:Y.559 Water bridges: A:R.541, A:R.541 Salt bridges: A:R.541, A:H.560 ASP.26: 11 residues within 4Å: Chain B: D.394, D.460, G.525, N.526, R.541, Y.559, H.560, Y.707 Ligands: ZN.21, ZN.22, GLU.25 11 PLIP interactions: 5 Ligand-Ligand interactions, 6 interactions with chain B Hydrogen bonds: E.25, D.26, D.26, D.26, D.26, B:N.526 Hydrophobic interactions: B:Y.559 Water bridges: B:R.541, B:R.541 Salt bridges: B:R.541, B:H.560

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Navratil, M. et al., Structural and biochemical characterization of the folyl-poly-gamma-l-glutamate hydrolyzing activity of human glutamate carboxypeptidase II. Febs J. (2014)

Release Date

2014-06-18

Peptides

Glutamate carboxypeptidase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glutamate carboxypeptidase 2