SMTL ID : 4p4b.1

X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a phosphoramidate inhibitor CTT54

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 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.33, Q.36, Q.52, S.55, Q.56, E.59 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.78, T.80, H.81, T.306 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: Y.84, E.94, I.95, N.97 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 6 residues within 4Å: Chain B: N.33, Q.36, Q.52, S.55, Q.56, E.59 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain B: N.78, T.80, H.81, T.306 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 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: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.4: 6 residues within 4Å: Chain A: S.429, L.430, N.433, P.551, Q.608, D.609 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Q.608, A:Q.608 Hydrogen bonds: A:D.609, A:D.609 NAG-NAG-BMA.16: 6 residues within 4Å: Chain B: S.429, L.430, N.433, P.551, Q.608, D.609 3 PLIP interactions: 3 interactions with chain B Water bridges: B:Q.608, B:Q.608 Hydrogen bonds: B:D.609, B:D.609

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.5: 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 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.233, B:R.311, B:R.311 Water bridges: B:H.69, B:R.311 NAG-NAG-BMA-MAN.17: 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.233, A:R.311, A:R.311 Water bridges: A:H.69, A:R.311

4 x ZN: ZINC ION(Non-covalent)

ZN.6: 6 residues within 4Å: Chain A: D.344, E.382, Y.509, H.510 Ligands: ZN.7, 2G2.12 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.344, A:E.382, A:E.382, A:H.510 ZN.7: 7 residues within 4Å: Chain A: H.334, D.344, E.381, E.382, D.410 Ligands: ZN.6, 2G2.12 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.334, A:D.344, A:D.410, A:D.410 ZN.18: 6 residues within 4Å: Chain B: D.344, E.382, Y.509, H.510 Ligands: ZN.19, 2G2.24 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.344, B:E.382, B:E.382, B:H.510 ZN.19: 7 residues within 4Å: Chain B: H.334, D.344, E.381, E.382, D.410 Ligands: ZN.18, 2G2.24 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.334, B:D.344, B:D.410, B:D.410

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: 5 interactions with chain A Metal complexes: A:T.226, A:Y.229, A:E.390, A:E.390, A:E.393 CA.20: 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.9: 5 residues within 4Å: Chain A: N.408, D.410, R.491, R.493, R.537 Ligand excluded by PLIP CL.21: 5 residues within 4Å: Chain B: N.408, D.410, R.491, R.493, R.537 Ligand excluded by PLIP

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

NAG.10: 2 residues within 4Å: Chain A: N.152, S.154 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.152, 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.22: 2 residues within 4Å: Chain B: N.152, S.154 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.152, 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

2 x 2G2: L-gamma-glutamyl-O-[(S)-{[(1S)-1,3-dicarboxypropyl]amino}(hydroxy)phosphoryl]-L-serine(Non-covalent)

2G2.12: 23 residues within 4Å: Chain A: R.167, Y.191, Q.211, N.214, H.334, D.344, E.381, E.382, G.384, L.385, D.410, G.475, N.476, R.491, R.493, S.504, Y.506, Y.509, H.510, K.656, Y.657 Ligands: ZN.6, ZN.7 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:L.385, A:Y.509, A:Y.509 Hydrogen bonds: A:Q.211, A:N.214, A:G.475, A:N.476, A:S.504, A:Y.506, A:Y.509, A:Y.509 Water bridges: A:R.167, A:R.491, A:R.493, A:R.493, A:K.656 Salt bridges: A:R.167, A:R.491, A:R.493, A:H.510, A:K.656 2G2.24: 23 residues within 4Å: Chain B: R.167, Y.191, Q.211, N.214, H.334, D.344, E.381, E.382, G.384, L.385, D.410, G.475, N.476, R.491, R.493, S.504, Y.506, Y.509, H.510, K.656, Y.657 Ligands: ZN.18, ZN.19 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:L.385, B:Y.509, B:Y.509 Hydrogen bonds: B:Q.211, B:N.214, B:G.475, B:N.476, B:S.504, B:Y.506, B:Y.509, B:Y.509 Water bridges: B:R.167, B:R.491, B:R.493, B:R.493, B:K.656 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

Novakova, Z. et al., Design of composite inhibitors targeting glutamate carboxypeptidase II: the importance of effector functionalities. Febs J. (2016)

Release Date

2015-05-20

Peptides

Glutamate carboxypeptidase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glutamate carboxypeptidase 2

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