SMTL ID : 6h7y.1

X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a inhibitor RNA 1-79-1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.81 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: 3 residues within 4Å: Chain A: N.33, 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: 4 residues within 4Å: Chain A: Y.84, E.94, I.95, N.97 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 3 residues within 4Å: Chain B: N.33, Q.52, Q.56 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Q.52 Hydrogen bonds: B:S.55 NAG-NAG.27: 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- 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: 6 residues within 4Å: Chain A: L.430, N.433, P.551, Q.608, D.609, D.611 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.609, A:D.611 NAG-NAG-BMA-MAN.28: 6 residues within 4Å: Chain B: L.430, N.433, P.551, Q.608, D.609, D.611 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.609, B:D.611

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.4: 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:L.67 NAG-NAG-BMA-MAN-MAN.29: 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:L.67

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

NAG.5: 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.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.30: 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.31: 2 residues within 4Å: Chain B: N.152, S.154 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.154 NAG.32: 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, FVZ.24 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.11 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.11 ZN.33: 5 residues within 4Å: Chain B: D.344, E.382, H.510 Ligands: ZN.34, FVZ.49 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.27 ZN.34: 6 residues within 4Å: Chain B: H.334, D.344, E.381, E.382, D.410 Ligands: ZN.33 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.27

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: 5 interactions with chain A Metal complexes: A:T.226, A:Y.229, A:E.390, A:E.390, A:E.393 CA.35: 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

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.25: 4 residues within 4Å: Chain A: Y.191, G.505, Y.509 Ligands: FVZ.24 Ligand excluded by PLIP CL.36: 4 residues within 4Å: Chain B: N.408, D.410, R.491, R.493 Ligand excluded by PLIP CL.50: 4 residues within 4Å: Chain B: Y.191, G.505, Y.509 Ligands: FVZ.49 Ligand excluded by PLIP

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

EDO.12: 3 residues within 4Å: Chain A: D.566, K.567, S.570 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.570 Water bridges: A:D.566, A:D.566 EDO.13: 4 residues within 4Å: Chain A: E.25, K.28, P.525, M.526 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.25, A:P.525 Water bridges: A:E.25 EDO.14: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.16: 3 residues within 4Å: Chain A: K.281, V.282, P.283 No protein-ligand interaction detected (PLIP) EDO.17: 2 residues within 4Å: Chain A: E.44, F.47 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.313, A:Y.313 EDO.37: 3 residues within 4Å: Chain B: D.566, K.567, S.570 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.570 Water bridges: B:D.566, B:D.566 EDO.38: 4 residues within 4Å: Chain B: E.25, K.28, P.525, M.526 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.25, B:P.525 Water bridges: B:E.25 EDO.39: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.40: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.41: 3 residues within 4Å: Chain B: K.281, V.282, P.283 No protein-ligand interaction detected (PLIP) EDO.42: 2 residues within 4Å: Chain B: E.44, F.47 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.313, B:Y.313

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

TAM.18: 6 residues within 4Å: Chain A: T.226, P.227, Y.229, R.238 Chain B: L.636, R.687 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.636, A:P.227 Hydrogen bonds: B:R.687, B:R.687, A:R.238 Water bridges: A:Y.229 TAM.19: 4 residues within 4Å: Chain A: S.458, R.468, S.470, W.498 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.498 Hydrogen bonds: A:S.458 TAM.43: 6 residues within 4Å: Chain A: L.636, R.687 Chain B: T.226, P.227, Y.229, R.238 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:P.227, A:L.636 Hydrogen bonds: B:R.238, A:R.687, A:R.687 Water bridges: B:Y.229 TAM.44: 4 residues within 4Å: Chain B: S.458, R.468, S.470, W.498 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.498 Hydrogen bonds: B:S.458

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

PEG.20: 6 residues within 4Å: Chain A: Y.328, W.391, L.398 Chain B: E.701, E.705, V.706 No protein-ligand interaction detected (PLIP) PEG.21: 4 residues within 4Å: Chain A: Y.582, S.679, G.683 Chain B: Y.236 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.679 PEG.22: 3 residues within 4Å: Chain A: L.40, G.42, K.79 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.79 Water bridges: A:D.113 PEG.45: 6 residues within 4Å: Chain A: E.701, E.705, V.706 Chain B: Y.328, W.391, L.398 No protein-ligand interaction detected (PLIP) PEG.46: 4 residues within 4Å: Chain A: Y.236 Chain B: Y.582, S.679, G.683 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.679 PEG.47: 3 residues within 4Å: Chain B: L.40, G.42, K.79 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.79 Water bridges: B:D.113

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.23: 11 residues within 4Å: Chain A: D.326, R.327, E.401, R.402, F.627 Chain B: R.327, D.623, Q.624, F.627, T.702 Ligands: PGE.48 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.327, A:R.327, A:R.402, B:D.623 PGE.48: 11 residues within 4Å: Chain A: R.327, D.623, Q.624, F.627, T.702 Chain B: D.326, R.327, E.401, R.402, F.627 Ligands: PGE.23 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.327, B:R.327, B:R.402, A:D.623

2 x FVZ: (2~{S})-2-[[(2~{S})-6-[(4-fluorophenyl)amino]-1-oxidanyl-1,6-bis(oxidanylidene)hexan-2-yl]carbamoylamino]pentanedioic acid(Non-covalent)

FVZ.24: 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, F.503, S.504, G.505, Y.509, H.510, K.656, Y.657 Ligands: ZN.8, CL.25 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:Y.509, A:Y.657 Hydrogen bonds: A:N.214, A:G.475, A:G.475, A:G.475, A:N.476, A:G.505, A:Y.509 Water bridges: A:N.214, A:D.344, 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 FVZ.49: 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, F.503, S.504, G.505, Y.509, H.510, K.656, Y.657 Ligands: ZN.33, CL.50 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:Y.509, B:Y.657 Hydrogen bonds: B:N.214, B:G.475, B:G.475, B:G.475, B:N.476, B:G.505, B:Y.509 Water bridges: B:N.214, B:D.344, 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

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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