SMTL ID : 8bol.1

X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with an inhibitor P18

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

4 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.1: 5 residues within 4Å: Chain A: N.33, Q.36, Q.52, S.55, Q.56 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 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, A:Q.608, A:Q.608 NAG-NAG-BMA.14: 5 residues within 4Å: Chain B: N.33, Q.36, Q.52, S.55, Q.56 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 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, B:Q.608, B:Q.608

2 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN.2: 10 residues within 4Å: Chain A: S.588, S.591, A.592, N.595, Q.697 Chain B: L.67, H.69, E.233, Y.234, R.311 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.233, B:R.311, B:R.311, B:L.67, B:L.67 Water bridges: B:H.69, B:H.69 NAG-NAG-BMA-MAN-MAN.15: 10 residues within 4Å: Chain A: L.67, H.69, E.233, Y.234, R.311 Chain B: S.588, S.591, A.592, N.595, Q.697 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.233, A:R.311, A:R.311, A:L.67, A:L.67 Water bridges: A:H.69, A:H.69

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.3: 4 residues within 4Å: Chain A: N.78, T.80, H.81, T.306 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain B: N.78, T.80, H.81, T.306 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-FUC.4: 5 residues within 4Å: Chain A: Y.84, E.94, I.95, N.97, L.100 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.84, A:L.100 NAG-NAG-BMA-FUC.17: 5 residues within 4Å: Chain B: Y.84, E.94, I.95, N.97, L.100 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.84, B:L.100

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, QWF.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.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.19: 6 residues within 4Å: Chain B: D.344, E.382, Y.509, H.510 Ligands: ZN.20, QWF.26 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.30 ZN.20: 6 residues within 4Å: Chain B: H.334, D.344, E.381, E.382, D.410 Ligands: ZN.19 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.30

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.21: 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.22: 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: 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.23: 2 residues within 4Å: Chain B: N.152, S.154 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.154 NAG.24: 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 NA: SODIUM ION(Non-functional Binders)

NA.12: 4 residues within 4Å: Chain A: Y.108, Y.199, T.515, E.517 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.199, A:T.515, A:T.515 NA.25: 4 residues within 4Å: Chain B: Y.108, Y.199, T.515, E.517 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.199, B:Y.199, B:T.515

2 x QWF: (2~{S})-2-[[(2~{S})-1-oxidanyl-1-oxidanylidene-6-[[(~{E},2~{S})-5-phenyl-2-[[4-[[2-[4,7,10-tris(2-hydroxy-2-oxoethyl)-1,4,7,10-tetrazacyclododec-1-yl]ethanoylamino]methyl]cyclohexyl]carbonylamino]pent-4-enoyl]amino]hexan-2-yl]carbamoylamino]pentanedioic acid(Non-covalent)

QWF.13: 25 residues within 4Å: Chain A: K.164, F.166, R.167, N.214, D.344, E.381, E.382, G.384, L.385, R.468, S.470, G.475, N.476, R.491, R.493, W.498, S.504, G.505, Y.509, H.510, N.655, K.656, Y.657, A.658 Ligands: ZN.6 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: A:K.164, A:L.385, A:Y.509, A:Y.657, A:A.658 Hydrogen bonds: A:N.214, A:S.470, A:G.475, A:G.475, A:G.475, A:N.476, A:Y.509, A:N.655 Water bridges: A:N.214, A:D.344, A:E.382, A:R.420, A:R.420, A:K.471, A:R.491, A:R.493, A:K.496, A:G.505, A:G.505, A:G.505, A:K.656, A:G.659 Salt bridges: A:R.167, A:R.491, A:R.493, A:K.496, A:H.510, A:K.656 QWF.26: 25 residues within 4Å: Chain B: K.164, F.166, R.167, N.214, D.344, E.381, E.382, G.384, L.385, R.468, S.470, G.475, N.476, R.491, R.493, W.498, S.504, G.505, Y.509, H.510, N.655, K.656, Y.657, A.658 Ligands: ZN.19 33 PLIP interactions: 33 interactions with chain B Hydrophobic interactions: B:K.164, B:L.385, B:Y.509, B:Y.657, B:A.658 Hydrogen bonds: B:N.214, B:S.470, B:G.475, B:G.475, B:G.475, B:N.476, B:Y.509, B:N.655 Water bridges: B:N.214, B:D.344, B:E.382, B:R.420, B:R.420, B:K.471, B:R.491, B:R.493, B:K.496, B:G.505, B:G.505, B:G.505, B:K.656, B:G.659 Salt bridges: B:R.167, B:R.491, B:R.493, B:K.496, B:H.510, B:K.656

Links

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Citation

Schafer, M. et al., Structure-Activity Relationships and Biological Insights into PSMA-617 and Its Derivatives with Modified Lipophilic Linker Regions. Acs Omega (2025)

Release Date

2023-11-29

Peptides

Glutamate carboxypeptidase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glutamate carboxypeptidase 2

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