SMTL ID : 6h7z.1

X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a inhibitor RNA 2-65-1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

8 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.33, Q.36, Q.52, S.55, Q.56 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.52 Water bridges: A:S.55 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.4: 5 residues within 4Å: Chain A: W.203, N.416, N.501, F.522, Y.523 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.501 NAG-NAG.23: 5 residues within 4Å: Chain B: N.33, Q.36, Q.52, S.55, Q.56 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Q.52 Water bridges: B:S.55 NAG-NAG.24: 4 residues within 4Å: Chain B: N.78, T.80, H.81, T.306 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 4 residues within 4Å: Chain B: Y.84, E.94, I.95, N.97 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 5 residues within 4Å: Chain B: W.203, N.416, N.501, F.522, Y.523 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.501

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.5: 7 residues within 4Å: Chain A: S.429, L.430, N.433, P.551, Q.608, D.609 Ligands: EDO.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.609 NAG-NAG-BMA.27: 7 residues within 4Å: Chain B: S.429, L.430, N.433, P.551, Q.608, D.609 Ligands: EDO.38 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.609

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.6: 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 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.233, B:R.311, B:R.311, B:H.69 Water bridges: B:H.69, B:E.66 NAG-NAG-BMA-MAN-MAN.28: 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.233, A:R.311, A:R.311, A:H.69 Water bridges: A:H.69, A:E.66

4 x ZN: ZINC ION(Non-covalent)

ZN.7: 5 residues within 4Å: Chain A: D.344, E.382, H.510 Ligands: ZN.8, FVW.22 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.10 ZN.8: 6 residues within 4Å: Chain A: H.334, D.344, E.381, E.382, D.410 Ligands: ZN.7 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.10 ZN.29: 5 residues within 4Å: Chain B: D.344, E.382, H.510 Ligands: ZN.30, FVW.44 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.31 ZN.30: 6 residues within 4Å: Chain B: H.334, D.344, E.381, E.382, D.410 Ligands: ZN.29 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.31

2 x CA: CALCIUM ION(Non-covalent)

CA.9: 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.31: 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.10: 4 residues within 4Å: Chain A: N.408, D.410, R.491, R.493 Ligand excluded by PLIP CL.32: 4 residues within 4Å: Chain B: N.408, D.410, R.491, R.493 Ligand excluded by PLIP

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

NAG.11: 2 residues within 4Å: Chain A: N.152, S.154 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.154 NAG.33: 2 residues within 4Å: Chain B: N.152, S.154 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.154

6 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.12: 4 residues within 4Å: Chain A: E.701, E.705 Chain B: W.391, L.398 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.328, A:E.701 Water bridges: A:S.704 PEG.20: 3 residues within 4Å: Chain A: K.29, Y.32, Y.516 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.516 PEG.21: 6 residues within 4Å: Chain A: R.555, A.558, V.559, R.562, V.593, T.597 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.558 PEG.34: 4 residues within 4Å: Chain A: W.391, L.398 Chain B: E.701, E.705 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.701, A:Y.328 Water bridges: B:S.704 PEG.42: 3 residues within 4Å: Chain B: K.29, Y.32, Y.516 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.516 PEG.43: 6 residues within 4Å: Chain B: R.555, A.558, V.559, R.562, V.593, T.597 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.558

12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.13: 2 residues within 4Å: Chain A: R.238 Chain B: R.687 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.238 Water bridges: B:R.687, B:R.687 EDO.14: 3 residues within 4Å: Chain A: G.42, Y.76, K.79 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.42, A:K.79, A:K.79 EDO.15: 4 residues within 4Å: Chain A: S.470, K.471, A.658, G.659 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.471, A:K.471, A:G.659 Water bridges: A:S.470, A:K.471 EDO.16: 5 residues within 4Å: Chain A: V.549, L.550, P.551, F.552 Ligands: NAG-NAG-BMA.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.547, A:S.547, A:F.552 EDO.17: 3 residues within 4Å: Chain A: E.598, I.599, K.602 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.602, A:K.602 Water bridges: A:N.595 EDO.18: 5 residues within 4Å: Chain A: R.555, S.601, S.604, E.605, Q.608 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.555, A:S.601, A:Q.608 EDO.35: 2 residues within 4Å: Chain A: R.687 Chain B: R.238 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.238 Water bridges: A:R.687, A:R.687 EDO.36: 3 residues within 4Å: Chain B: G.42, Y.76, K.79 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.42, B:K.79, B:K.79 EDO.37: 4 residues within 4Å: Chain B: S.470, K.471, A.658, G.659 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.471, B:K.471, B:G.659 Water bridges: B:S.470, B:K.471 EDO.38: 5 residues within 4Å: Chain B: V.549, L.550, P.551, F.552 Ligands: NAG-NAG-BMA.27 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.547, B:S.547, B:F.552 EDO.39: 3 residues within 4Å: Chain B: E.598, I.599, K.602 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.602, B:K.602 Water bridges: B:N.595 EDO.40: 5 residues within 4Å: Chain B: R.555, S.601, S.604, E.605, Q.608 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.555, B:S.601, B:Q.608

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.19: 3 residues within 4Å: Chain A: R.468, W.498, E.499 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.499 TRS.41: 3 residues within 4Å: Chain B: R.468, W.498, E.499 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.499

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

FVW.22: 24 residues within 4Å: Chain A: G.163, K.164, V.165, F.166, R.167, N.214, D.344, E.381, E.382, G.384, L.385, E.414, G.475, N.476, R.491, R.493, W.498, S.504, G.505, Y.509, H.510, K.656, Y.657 Ligands: ZN.7 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:Y.509, A:Y.657, A:Y.657 Hydrogen bonds: A:N.214, A:R.420, A:G.475, A:G.475, A:N.476, A:R.493, A:Y.509 Water bridges: A:Q.211, A:N.214, A:D.344, A:R.491, A:K.656 Salt bridges: A:R.167, A:R.491, A:R.493, A:H.510, A:K.656 FVW.44: 24 residues within 4Å: Chain B: G.163, K.164, V.165, F.166, R.167, N.214, D.344, E.381, E.382, G.384, L.385, E.414, G.475, N.476, R.491, R.493, W.498, S.504, G.505, Y.509, H.510, K.656, Y.657 Ligands: ZN.29 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:Y.509, B:Y.657, B:Y.657 Hydrogen bonds: B:N.214, B:R.420, B:G.475, B:G.475, B:N.476, B:R.493, B:Y.509 Water bridges: B:Q.211, B:N.214, B:D.344, B:R.491, 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

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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