SMTL ID : 5f09.1

Structure of inactive GCPII mutant in complex with beta-citryl glutamate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 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.65, Q.84, S.87, Q.88, E.91 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: Y.116, E.126, I.127, N.129 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 5 residues within 4Å: Chain B: N.65, Q.84, S.87, Q.88, E.91 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain B: Y.116, E.126, I.127, N.129 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.3: 5 residues within 4Å: Chain A: S.461, L.462, N.465, P.583, Q.640 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.587 NAG-NAG-BMA.16: 5 residues within 4Å: Chain B: S.461, L.462, N.465, P.583, Q.640 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.587

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: 9 residues within 4Å: Chain A: S.620, S.623, A.624, N.627, Q.729 Chain B: H.101, E.265, Y.266, R.343 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.265, B:R.343, B:R.343, B:E.265 Water bridges: B:H.101, B:R.343, B:R.343 NAG-NAG-BMA-MAN.17: 9 residues within 4Å: Chain A: H.101, E.265, Y.266, R.343 Chain B: S.620, S.623, A.624, N.627, Q.729 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.265, A:R.343, A:R.343, A:E.265 Water bridges: A:H.101, A:R.343, A:R.343

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

NAG.5: 3 residues within 4Å: Chain A: N.110, H.113, T.338 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.110 NAG.6: 2 residues within 4Å: Chain A: N.184, S.186 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.186 NAG.7: 4 residues within 4Å: Chain A: W.235, N.448, F.554, Y.555 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.235, A:Y.555 Hydrogen bonds: A:W.235, A:F.554 Water bridges: A:N.448, A:N.448 NAG.18: 3 residues within 4Å: Chain B: N.110, H.113, T.338 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.110 NAG.19: 2 residues within 4Å: Chain B: N.184, S.186 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.186 NAG.20: 4 residues within 4Å: Chain B: W.235, N.448, F.554, Y.555 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.235, B:Y.555 Hydrogen bonds: B:W.235, B:F.554 Water bridges: B:N.448, B:N.448

4 x ZN: ZINC ION(Non-covalent)

ZN.8: 5 residues within 4Å: Chain A: D.376, E.414, H.542 Ligands: ZN.9, BC8.12 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.376, A:E.414, A:H.542, H2O.1, H2O.2 ZN.9: 5 residues within 4Å: Chain A: H.366, D.376, E.414, D.442 Ligands: ZN.8 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.366, A:D.376, A:D.442, H2O.1, H2O.12 ZN.21: 5 residues within 4Å: Chain B: D.376, E.414, H.542 Ligands: ZN.22, BC8.25 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.376, B:E.414, B:H.542, H2O.22, H2O.23 ZN.22: 5 residues within 4Å: Chain B: H.366, D.376, E.414, D.442 Ligands: ZN.21 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.366, B:D.376, B:D.442, H2O.22, H2O.33

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

CL.10: 5 residues within 4Å: Chain A: N.440, D.442, R.523, R.525, R.569 Ligand excluded by PLIP CL.23: 5 residues within 4Å: Chain B: N.440, D.442, R.523, R.525, R.569 Ligand excluded by PLIP

2 x CA: CALCIUM ION(Non-covalent)

CA.11: 4 residues within 4Å: Chain A: T.258, Y.261, E.422, E.425 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:T.258, A:Y.261, A:E.422, A:E.422, A:E.425 CA.24: 4 residues within 4Å: Chain B: T.258, Y.261, E.422, E.425 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:T.258, B:Y.261, B:E.422, B:E.422, B:E.425

2 x BC8: beta-citryl-L-glutamic acid(Non-covalent)

BC8.12: 19 residues within 4Å: Chain A: F.198, R.199, N.246, D.376, A.413, E.414, G.416, L.417, D.442, S.506, G.507, N.508, R.523, R.525, Y.541, H.542, K.688, Y.689 Ligands: ZN.8 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:N.508, A:Y.689 Hydrogen bonds: A:N.246, A:E.414, A:S.506, A:N.508, A:Y.541 Water bridges: A:R.199, A:N.246, A:G.507, A:R.523, A:R.523, A:R.523 Salt bridges: A:R.199, A:R.523, A:R.525, A:H.542, A:K.688 BC8.25: 19 residues within 4Å: Chain B: F.198, R.199, N.246, D.376, A.413, E.414, G.416, L.417, D.442, S.506, G.507, N.508, R.523, R.525, Y.541, H.542, K.688, Y.689 Ligands: ZN.21 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:N.508, B:Y.689 Hydrogen bonds: B:N.246, B:E.414, B:E.414, B:S.506, B:N.508, B:Y.541 Water bridges: B:R.199, B:N.246, B:G.507, B:R.523, B:R.523, B:R.523 Salt bridges: B:R.199, B:R.523, B:R.525, B:H.542, B:K.688

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.13: 7 residues within 4Å: Chain A: P.667, L.668 Chain B: R.270, P.667, P.674, F.675 Ligands: PGE.26 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.270, B:P.667 PGE.26: 7 residues within 4Å: Chain A: R.270, P.667, P.674, F.675 Chain B: P.667, L.668 Ligands: PGE.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.270, A:P.667

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Navratil, M. et al., Comparison of human glutamate carboxypeptidases II and III reveals their divergent substrate specificities. Febs J. (2016)

Release Date

2016-06-01

Peptides

Glutamate carboxypeptidase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glutamate carboxypeptidase 2