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- PDB-7bfz: X-ray structure of human prostate-specific membrane antigen(PSMA)... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7bfz | ||||||
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Title | X-ray structure of human prostate-specific membrane antigen(PSMA) in complex with a inhibitor Glu-490 | ||||||
![]() | Glutamate carboxypeptidase 2 | ||||||
![]() | HYDROLASE / glutamate carboxypeptidase II (GCPII) / NAALADase / prostate-specific membrane antigen (PSMA) / inhibitor | ||||||
Function / homology | ![]() Ac-Asp-Glu binding / tetrahydrofolyl-poly(glutamate) polymer binding / glutamate carboxypeptidase II / folic acid-containing compound metabolic process / C-terminal protein deglutamylation / Aspartate and asparagine metabolism / dipeptidase activity / metallocarboxypeptidase activity / carboxypeptidase activity / peptidase activity ...Ac-Asp-Glu binding / tetrahydrofolyl-poly(glutamate) polymer binding / glutamate carboxypeptidase II / folic acid-containing compound metabolic process / C-terminal protein deglutamylation / Aspartate and asparagine metabolism / dipeptidase activity / metallocarboxypeptidase activity / carboxypeptidase activity / peptidase activity / cell surface / proteolysis / extracellular exosome / membrane / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rakhimbekova, A. / Motlova, L. / Barinka, C. | ||||||
![]() | ![]() Title: A prostate-specific membrane antigen activated molecular rotor for real-time fluorescence imaging. Authors: Zhang, J. / Rakhimbekova, A. / Duan, X. / Yin, Q. / Foss, C.A. / Fan, Y. / Xu, Y. / Li, X. / Cai, X. / Kutil, Z. / Wang, P. / Yang, Z. / Zhang, N. / Pomper, M.G. / Wang, Y. / Barinka, C. / Yang, X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 320.3 KB | Display | ![]() |
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PDB format | ![]() | 255.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3bi1S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 79614.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The missing amino acids were not possible to model into electron density map due to their flexibility. Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 5 types, 7 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...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 | Source method: isolated from a genetically manipulated source #4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...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 | Source method: isolated from a genetically manipulated source #9: Sugar | |
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-Non-polymers , 8 types, 478 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/TKZ.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/TKZ.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | #7: Chemical | ChemComp-CA / | #8: Chemical | ChemComp-CL / | #10: Chemical | #11: Chemical | ChemComp-PEG / | #12: Chemical | #13: Chemical | ChemComp-TKZ / ((( | #14: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62.68 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 34% (v/v) pentaerythritol propoxylate PO/OH 5/4 1 % (w/v) PEG 3350 100 mM Tris-HCl, pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Mar 1, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→50 Å / Num. obs: 109170 / % possible obs: 99.6 % / Redundancy: 4.5 % / CC1/2: 0.999 / Net I/σ(I): 14.43 |
Reflection shell | Resolution: 1.73→1.83 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 1.99 / Num. unique obs: 17360 / CC1/2: 0.869 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3BI1 Resolution: 1.73→46.96 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.966 / SU B: 3.497 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 124.88 Å2 / Biso mean: 36.467 Å2 / Biso min: 15.82 Å2
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Refinement step | Cycle: final / Resolution: 1.73→46.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.73→1.774 Å / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 17.7568 Å / Origin y: 49.355 Å / Origin z: 44.7393 Å
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