SMTL ID : 6hkj.1

X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a inhibitor RNA 2-19-1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 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: 4 residues within 4Å: Chain A: N.33, Q.36, Q.52, Q.56 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.52 Hydrogen bonds: A:S.55 NAG-NAG.2: 5 residues within 4Å: Chain A: S.429, L.430, N.433, P.551, Q.608 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.608 NAG-NAG.15: 4 residues within 4Å: Chain B: N.33, Q.36, Q.52, Q.56 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Q.52 Hydrogen bonds: B:S.55 NAG-NAG.16: 5 residues within 4Å: Chain B: S.429, L.430, N.433, P.551, Q.608 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.608

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.3: 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 4 PLIP interactions: 4 interactions with chain B Water bridges: B:E.233, B:E.233, B:H.69 Hydrogen bonds: B:E.233, B:R.311, 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 4 PLIP interactions: 4 interactions with chain A Water bridges: A:E.233, A:E.233, A:H.69 Hydrogen bonds: A:E.233, A:R.311, A:R.311

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

NAG.4: 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.5: 4 residues within 4Å: Chain A: Y.84, E.94, I.95, N.97 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.84, A:E.94, A:E.94, A:N.97 NAG.6: 2 residues within 4Å: Chain A: N.152, S.154 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.154 NAG.7: 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.18: 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.19: 4 residues within 4Å: Chain B: Y.84, E.94, I.95, N.97 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.84, B:E.94, B:E.94, B:N.97 NAG.20: 2 residues within 4Å: Chain B: N.152, S.154 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.154 NAG.21: 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

4 x ZN: ZINC ION(Non-covalent)

ZN.8: 5 residues within 4Å: Chain A: D.344, E.382, H.510 Ligands: ZN.9, G8W.13 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.5 ZN.9: 6 residues within 4Å: Chain A: H.334, D.344, E.381, E.382, D.410 Ligands: ZN.8 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.5 ZN.22: 5 residues within 4Å: Chain B: D.344, E.382, H.510 Ligands: ZN.23, G8W.27 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.20 ZN.23: 6 residues within 4Å: Chain B: H.334, D.344, E.381, E.382, D.410 Ligands: ZN.22 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.20

2 x CA: CALCIUM ION(Non-covalent)

CA.10: 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.24: 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.18

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

CL.11: 4 residues within 4Å: Chain A: N.408, D.410, R.491, R.493 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain A: Y.191, G.505, Y.509 Ligands: G8W.13 Ligand excluded by PLIP CL.25: 4 residues within 4Å: Chain B: N.408, D.410, R.491, R.493 Ligand excluded by PLIP CL.28: 4 residues within 4Å: Chain B: Y.191, G.505, Y.509 Ligands: G8W.27 Ligand excluded by PLIP

2 x TAM: TRIS(HYDROXYETHYL)AMINOMETHANE(Non-covalent)

TAM.12: 3 residues within 4Å: Chain A: S.458, R.468, W.498 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.498 Hydrogen bonds: A:S.458 TAM.26: 3 residues within 4Å: Chain B: S.458, R.468, W.498 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.498 Hydrogen bonds: B:S.458

2 x G8W: (2~{S})-2-[[(2~{S})-6-[(6-fluoranylpyridin-3-yl)amino]-1-oxidanyl-1,6-bis(oxidanylidene)hexan-2-yl]carbamoylamino]pentanedioic acid(Non-covalent)

G8W.13: 22 residues within 4Å: Chain A: K.164, F.166, R.167, N.214, D.344, E.381, E.382, G.384, L.385, G.475, N.476, R.491, R.493, S.504, G.505, Y.509, H.510, N.655, K.656, Y.657 Ligands: ZN.8, CL.14 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Y.509 Hydrogen bonds: A:N.214, A:G.475, A:G.475, A:N.476, A:G.505, A:Y.509 Water bridges: A:N.214, A:D.344, A:R.420, A:R.491, A:K.656 Salt bridges: A:R.167, A:R.491, A:R.493, A:H.510, A:K.656 pi-Stacking: A:Y.657 G8W.27: 22 residues within 4Å: Chain B: K.164, F.166, R.167, N.214, D.344, E.381, E.382, G.384, L.385, G.475, N.476, R.491, R.493, S.504, G.505, Y.509, H.510, N.655, K.656, Y.657 Ligands: ZN.22, CL.28 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:Y.509 Hydrogen bonds: B:N.214, B:G.475, B:G.475, B:N.476, B:G.505, B:Y.509 Water bridges: B:N.214, B:D.344, B:R.420, B:R.491, B:K.656 Salt bridges: B:R.167, B:R.491, B:R.493, B:H.510, B:K.656 pi-Stacking: B:Y.657

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakajima, R. et al., 2-Aminoadipic Acid-C(O)-Glutamate Based Prostate-Specific Membrane Antigen Ligands for Potential Use as Theranostics. ACS Med Chem Lett (2018)

Release Date

2018-12-05

Peptides

Glutamate carboxypeptidase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glutamate carboxypeptidase 2

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