SMTL ID : 5o5r.1

X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a urea based inhibitor PSMA 1023

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

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.1: 6 residues within 4Å: Chain A: N.33, Q.36, Q.52, S.55, Q.56, E.59 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.52 Hydrogen bonds: A:S.55 Water bridges: A:E.59 NAG-NAG.16: 6 residues within 4Å: Chain B: N.33, Q.36, Q.52, S.55, Q.56, E.59 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Q.52 Hydrogen bonds: B:S.55 Water bridges: B:E.59

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

NAG-NAG-FUC.2: 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-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

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.3: 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-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

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: 11 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 Ligands: EDO.29 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.233, B:R.311, B:R.311, B:L.67, B:H.69 Water bridges: B:H.69, B:R.311 NAG-NAG-BMA-MAN-MAN.19: 11 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 Ligands: EDO.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.233, A:R.311, A:R.311, A:L.67, A:H.69 Water bridges: A:H.69, A:R.311

2 x 9OQ: (2~{S})-2-[[(2~{S})-6-[[(2~{S})-2-[[4-[[[(2~{R})-2-[[(2~{R})-2-[(6-fluoranylpyridin-3-yl)carbonylamino]-5-oxidanyl-5-oxidanylidene-pentanoyl]amino]-5-oxidanyl-5-oxidanylidene-pentanoyl]amino]methyl]phenyl]carbonylamino]-3-naphthalen-2-yl-propanoyl]amino]-1-oxidanyl-1-oxidanylidene-hexan-2-yl]carbamoylamino]pentanedioic acid(Non-covalent)

9OQ.5: 28 residues within 4Å: Chain A: E.140, K.164, F.166, R.167, N.214, D.344, E.381, E.382, G.384, L.385, E.414, R.420, G.475, N.476, R.491, R.493, F.503, S.504, G.505, Y.506, Y.509, H.510, N.655, K.656, Y.657, A.658, F.670 Ligands: ZN.8 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:Y.506, A:Y.509, A:Y.657, A:Y.657, A:A.658 Hydrogen bonds: A:N.214, A:R.420, A:R.420, 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:R.491, A:K.567, A:K.656 Salt bridges: A:R.167, A:R.491, A:R.493, A:H.510, A:K.656 pi-Stacking: A:F.503, A:Y.509 9OQ.20: 28 residues within 4Å: Chain B: E.140, K.164, F.166, R.167, N.214, D.344, E.381, E.382, G.384, L.385, E.414, R.420, G.475, N.476, R.491, R.493, F.503, S.504, G.505, Y.506, Y.509, H.510, N.655, K.656, Y.657, A.658, F.670 Ligands: ZN.23 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:Y.506, B:Y.509, B:Y.657, B:Y.657, B:A.658 Hydrogen bonds: B:N.214, B:R.420, B:R.420, B:G.475, B:G.475, B:G.475, B:N.476, B:Y.509, B:N.655 Water bridges: B:N.214, B:R.491, B:K.567, B:K.656 Salt bridges: B:R.167, B:R.491, B:R.493, B:H.510, B:K.656 pi-Stacking: B:F.503, B:Y.509

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

NAG.6: 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.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.15: 4 residues within 4Å: Chain A: N.78, T.80, H.81, T.306 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.78, A:T.80 Water bridges: A:Q.124, A:Q.124 NAG.21: 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.22: 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 NAG.30: 4 residues within 4Å: Chain B: N.78, T.80, H.81, T.306 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.78, B:T.80 Water bridges: B:Q.124, B:Q.124

4 x ZN: ZINC ION(Non-covalent)

ZN.8: 5 residues within 4Å: Chain A: D.344, E.382, H.510 Ligands: 9OQ.5, ZN.9 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.13 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.13 ZN.23: 5 residues within 4Å: Chain B: D.344, E.382, H.510 Ligands: 9OQ.20, ZN.24 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.37 ZN.24: 6 residues within 4Å: Chain B: H.334, D.344, E.381, E.382, D.410 Ligands: ZN.23 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.37

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.25: 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.11: 5 residues within 4Å: Chain A: N.408, D.410, R.491, R.493, R.537 Ligand excluded by PLIP CL.26: 5 residues within 4Å: Chain B: N.408, D.410, R.491, R.493, R.537 Ligand excluded by PLIP

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

PEG.12: 6 residues within 4Å: Chain A: L.374, W.391, L.398 Chain B: E.701, E.705, V.706 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.701 PEG.13: 3 residues within 4Å: Chain A: K.29, Y.32, Y.516 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.516 PEG.27: 6 residues within 4Å: Chain A: E.701, E.705, V.706 Chain B: L.374, W.391, L.398 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.701 PEG.28: 3 residues within 4Å: Chain B: K.29, Y.32, Y.516 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Y.516

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

EDO.14: 4 residues within 4Å: Chain A: Q.54, E.66, L.67 Ligands: NAG-NAG-BMA-MAN-MAN.19 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.54, A:L.67, A:L.67 EDO.29: 4 residues within 4Å: Chain B: Q.54, E.66, L.67 Ligands: NAG-NAG-BMA-MAN-MAN.4 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.54, B:L.67, B:L.67

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Motlova, L. et al., X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a urea based inhibitor PSMA 1023. To Be Published

Release Date

2018-06-13

Peptides

Glutamate carboxypeptidase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glutamate carboxypeptidase 2

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