SMTL ID : 2cij.1

membrane-bound glutamate carboxypeptidase II (GCPII) with bound methionine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 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: 3 residues within 4Å: Chain A: N.33, Q.36, Q.52 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.3: 3 residues within 4Å: Chain A: S.429, N.433, P.551 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain B: N.33, Q.36, Q.52 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) NAG-NAG.15: 3 residues within 4Å: Chain B: S.429, N.433, P.551 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: 9 residues within 4Å: Chain A: S.588, S.591, A.592, N.595, Q.697 Chain B: H.69, E.233, Y.234, R.311 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.233, B:E.233, B:R.311 NAG-NAG-BMA-MAN.16: 9 residues within 4Å: Chain A: 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:E.233, A:R.311

2 x MET: METHIONINE(Non-covalent)

MET.5: 12 residues within 4Å: Chain A: R.167, N.214, E.381, E.382, G.384, L.385, G.475, Y.509, H.510, K.656, Y.657 Ligands: ZN.6 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:E.381, A:Y.509 Water bridges: A:N.214, A:E.382, A:N.476, A:N.476, A:N.476 Salt bridges: A:R.167, A:H.510 MET.17: 12 residues within 4Å: Chain B: R.167, N.214, E.381, E.382, G.384, L.385, G.475, Y.509, H.510, K.656, Y.657 Ligands: ZN.18 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:E.381, B:Y.509 Water bridges: B:N.214, B:E.382, B:N.476, B:N.476, B:N.476 Salt bridges: B:R.167, B:H.510

4 x ZN: ZINC ION(Non-covalent)

ZN.6: 5 residues within 4Å: Chain A: D.344, E.382, H.510 Ligands: MET.5, ZN.7 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.9 ZN.7: 6 residues within 4Å: Chain A: H.334, D.344, E.381, E.382, D.410 Ligands: ZN.6 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.9 ZN.18: 5 residues within 4Å: Chain B: D.344, E.382, H.510 Ligands: MET.17, ZN.19 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.17 ZN.19: 6 residues within 4Å: Chain B: H.334, D.344, E.381, E.382, D.410 Ligands: ZN.18 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.17

2 x CA: CALCIUM ION(Non-covalent)

CA.8: 4 residues within 4Å: Chain A: T.226, Y.229, E.390, E.393 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.226, A:E.390, A:E.390, A:E.393, H2O.3 CA.20: 4 residues within 4Å: Chain B: T.226, Y.229, E.390, E.393 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.226, B:E.390, B:E.390, B:E.393, H2O.11

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

CL.9: 4 residues within 4Å: Chain A: N.408, D.410, R.491, R.537 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain B: N.408, D.410, R.491, R.537 Ligand excluded by PLIP

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

NAG.10: 4 residues within 4Å: Chain A: N.78, T.80, H.81, T.306 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.306 Hydrogen bonds: A:T.80 NAG.11: 2 residues within 4Å: Chain A: N.152, S.154 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.152 NAG.12: 4 residues within 4Å: Chain A: W.203, N.416, F.522, Y.523 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.203, A:Y.523 Hydrogen bonds: A:W.203, A:F.522 NAG.22: 4 residues within 4Å: Chain B: N.78, T.80, H.81, T.306 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.306 Hydrogen bonds: B:T.80 NAG.23: 2 residues within 4Å: Chain B: N.152, S.154 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.152 NAG.24: 4 residues within 4Å: Chain B: W.203, N.416, F.522, Y.523 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.203, B:Y.523 Hydrogen bonds: B:W.203, B:F.522

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mesters, J.R. et al., Glutamate Carboxypeptidase II. Handbook of Metalloproteins (2011)

Release Date

2007-03-27

Peptides

GLUTAMATE CARBOXYPEPTIDASE II: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

GLUTAMATE CARBOXYPEPTIDASE II

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