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Open data
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Basic information
Entry | Database: PDB / ID: 4cyh | ||||||
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Title | CYCLOPHILIN A COMPLEXED WITH DIPEPTIDE HIS-PRO | ||||||
![]() | CYCLOPHILIN A![]() | ||||||
![]() | ![]() ![]() ![]() | ||||||
Function / homology | ![]() negative regulation of protein K48-linked ubiquitination / negative regulation of viral life cycle / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Zhao, Y. / Ke, H. | ||||||
![]() | ![]() Title: Mechanistic implication of crystal structures of the cyclophilin-dipeptide complexes. Authors: Zhao, Y. / Ke, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 51.6 KB | Display | ![]() |
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PDB format | ![]() | 37.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related 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
#1: Protein | ![]() Mass: 17905.307 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P05092, UniProt: P62937*PLUS, ![]() |
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#2: Chemical | ChemComp-HIS / ![]() |
#3: Chemical | ChemComp-PRO / ![]() |
#4: Water | ChemComp-HOH / ![]() |
Nonpolymer details | THE RESIDUES 201 AND 202 REPRESENT A DIPEPTIDE BOUND TO CYCLOPHILI |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.18 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow![]() | *PLUS Temperature: 4 ℃ / pH: 8.5 / Method: microdialysis | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Highest resolution: 2.1 Å / Num. obs: 10112 / % possible obs: 86 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.038 |
Reflection | *PLUS % possible obs: 86.8 % / Num. measured all: 34148 |
Reflection shell | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 2.2 Å / % possible obs: 80.9 % |
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Processing
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Refinement | Resolution: 2.1→8 Å / σ(F): 2 /
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Displacement parameters | Biso mean: 19.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→8 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.177 / Rfactor Rfree![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 3.1 |