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Open data
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Basic information
Entry | Database: PDB / ID: 6buy | |||||||||
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Title | Crystal structure of porcine aminopeptidase-N with Glycine | |||||||||
![]() | Aminopeptidase N | |||||||||
![]() | HYDROLASE / ZINC AMINOPEPTIDASE | |||||||||
Function / homology | ![]() membrane alanyl aminopeptidase / peptide catabolic process / metalloaminopeptidase activity / peptide binding / virus receptor activity / angiogenesis / cell differentiation / proteolysis / extracellular space / zinc ion binding ...membrane alanyl aminopeptidase / peptide catabolic process / metalloaminopeptidase activity / peptide binding / virus receptor activity / angiogenesis / cell differentiation / proteolysis / extracellular space / zinc ion binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Chen, L. / Lin, Y.-L. / Li, F. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: The Rational Design of Therapeutic Peptides for Aminopeptidase N using a Substrate-Based Approach. Authors: Joshi, S. / Chen, L. / Winter, M.B. / Lin, Y.L. / Yang, Y. / Shapovalova, M. / Smith, P.M. / Liu, C. / Li, F. / LeBeau, A.M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 424.5 KB | Display | ![]() |
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PDB format | ![]() | 344.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.4 MB | Display | ![]() |
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Full document | ![]() | 3.4 MB | Display | |
Data in XML | ![]() | 46.2 KB | Display | |
Data in CIF | ![]() | 70.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6bv0C ![]() 6bv1C ![]() 6bv2C ![]() 6bv3C ![]() 6bv4C ![]() 4fkeS S: Starting model for refinement C: citing same article ( |
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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: 102692.266 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Sugars , 3 types, 11 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | #3: 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 #4: Sugar | |
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-Non-polymers , 4 types, 944 molecules ![](data/chem/img/GLY.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-GLY / | ||||
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#6: Chemical | ChemComp-SO4 / #7: Chemical | ChemComp-ZN / | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.53 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: 18% PEG3350, 200 MM LITHIUM SULFATE, 100 MM HEPES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 29, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 72167 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rsym value: 0.061 / Net I/σ(I): 20.11 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3.13 / Num. unique obs: 7492 / Rsym value: 0.464 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4FKE Resolution: 2.1→128.22 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.928 / SU B: 15.247 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R Free: 0.183 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.088 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→128.22 Å
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Refine LS restraints |
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