SMTL ID : 4mcr.1

A high resolution structure of human glutamate carboxypeptidase II (GCPII) in complex with folyltri-gamma-L-glutamic acid (pteroyltetra-gamma-L-glutamic acid)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 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.83, Q.86, Q.102, S.105, Q.106 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.102 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.13: 5 residues within 4Å: Chain B: N.83, Q.86, Q.102, S.105, Q.106 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Q.102 Hydrogen bonds: B:S.105 NAG-NAG.14: 5 residues within 4Å: Chain B: Y.134, E.144, I.145, F.146, N.147 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 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(Non-functional Binders)

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 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.283, B:R.361, B:R.361 Water bridges: B:H.119 NAG-NAG-BMA-MAN.16: 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.283, A:R.361, A:R.361 Water bridges: A:H.119

4 x ZN: ZINC ION(Non-covalent)

ZN.5: 5 residues within 4Å: Chain A: D.394, E.432, H.560 Ligands: ZN.6, 29D.12 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.394, A:E.432, A:E.432, A:H.560, H2O.17 ZN.6: 5 residues within 4Å: Chain A: H.384, D.394, E.432, D.460 Ligands: ZN.5 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.17 ZN.17: 5 residues within 4Å: Chain B: D.394, E.432, H.560 Ligands: ZN.18, 29D.24 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.41 ZN.18: 5 residues within 4Å: Chain B: H.384, D.394, E.432, D.460 Ligands: ZN.17 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.41

2 x CA: CALCIUM ION(Non-covalent)

CA.7: 4 residues within 4Å: Chain A: T.276, Y.279, E.440, E.443 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:T.276, A:Y.279, A:E.440, A:E.440, A:E.443 CA.19: 4 residues within 4Å: Chain B: T.276, Y.279, E.440, E.443 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:T.276, B:Y.279, B:E.440, B:E.440, B:E.443

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

CL.8: 5 residues within 4Å: Chain A: N.458, D.460, R.541, R.543, R.587 Ligand excluded by PLIP CL.20: 5 residues within 4Å: Chain B: N.458, D.460, R.541, R.543, R.587 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.128, T.130, H.131, T.356 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.356 Hydrogen bonds: A:T.130 NAG.10: 2 residues within 4Å: Chain A: N.202, S.204 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.204 Water bridges: A:N.202 NAG.11: 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.21: 4 residues within 4Å: Chain B: N.128, T.130, H.131, T.356 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.356 Hydrogen bonds: B:T.130 NAG.22: 2 residues within 4Å: Chain B: N.202, S.204 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.204 Water bridges: B:N.202 NAG.23: 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

2 x 29D: N-(4-{[(2-amino-4-oxo-3,4-dihydropteridin-6-yl)methyl]amino}benzoyl)-L-gamma-glutamyl-L-gamma-glutamyl-L-gamma-glutamyl-L-glutamic acid(Non-covalent)

29D.12: 24 residues within 4Å: Chain A: F.216, R.217, N.264, D.394, A.431, E.432, G.434, L.435, R.470, R.518, S.520, G.525, N.526, R.541, R.543, W.548, E.549, Y.559, H.560, N.705, K.706, Y.707, A.708 Ligands: ZN.5 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:Y.707, A:Y.707, A:A.708 Hydrogen bonds: A:N.264, A:E.432, A:R.518, A:N.526, A:E.549, A:Y.559 Water bridges: A:N.264, A:R.470, A:R.470, A:V.471, A:R.541, A:R.541, A:K.706, A:Y.707, A:G.709, A:G.709 Salt bridges: A:R.217, A:R.470, A:R.541, A:R.543, A:E.549, A:H.560, A:K.706 pi-Stacking: A:W.548, A:W.548, A:W.548 pi-Cation interactions: A:R.518, A:W.548 29D.24: 24 residues within 4Å: Chain B: F.216, R.217, N.264, D.394, A.431, E.432, G.434, L.435, R.470, R.518, S.520, G.525, N.526, R.541, R.543, W.548, E.549, Y.559, H.560, N.705, K.706, Y.707, A.708 Ligands: ZN.17 32 PLIP interactions: 32 interactions with chain B Hydrophobic interactions: B:Y.707, B:Y.707, B:A.708 Hydrogen bonds: B:N.264, B:E.432, B:R.518, B:G.525, B:N.526, B:E.549, B:Y.559 Water bridges: B:N.264, B:R.470, B:R.470, B:V.471, B:R.541, B:R.541, B:K.706, B:Y.707, B:G.709, B:G.709 Salt bridges: B:R.217, B:R.470, B:R.541, B:R.543, B:E.549, B:H.560, B:K.706 pi-Stacking: B:W.548, B:W.548, B:W.548 pi-Cation interactions: B:R.518, B:W.548

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

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