+Open data
-Basic information
Entry | Database: PDB / ID: 5cyh | ||||||
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Title | CYCLOPHILIN A COMPLEXED WITH DIPEPTIDE GLY-PRO | ||||||
Components | CYCLOPHILIN A | ||||||
Keywords | ISOMERASE / CYCLOPHILIN / COMPLEX / BINDING PROTEIN FOR CYCLOSPORIN A / (ISOMERASE-DIPEPTIDE) COMPLEX | ||||||
Function / homology | Function and homology information 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 / heparan sulfate binding / regulation of viral genome replication / leukocyte chemotaxis / endothelial cell activation / virion binding ...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 / heparan sulfate binding / regulation of viral genome replication / leukocyte chemotaxis / endothelial cell activation / virion binding / Basigin interactions / negative regulation of stress-activated MAPK cascade / cyclosporin A binding / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Calcineurin activates NFAT / viral release from host cell / positive regulation of viral genome replication / Binding and entry of HIV virion / protein peptidyl-prolyl isomerization / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of protein dephosphorylation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / activation of protein kinase B activity / neutrophil chemotaxis / negative regulation of protein phosphorylation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / positive regulation of protein secretion / Assembly Of The HIV Virion / negative regulation of protein kinase activity / Budding and maturation of HIV virion / neuron differentiation / platelet activation / platelet aggregation / SARS-CoV-1 activates/modulates innate immune responses / unfolded protein binding / integrin binding / protein folding / Platelet degranulation / positive regulation of NF-kappaB transcription factor activity / cellular response to oxidative stress / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / positive regulation of MAPK cascade / response to hypoxia / positive regulation of protein phosphorylation / intracellular membrane-bounded organelle / focal adhesion / apoptotic process / Neutrophil degranulation / protein-containing complex / RNA binding / extracellular space / extracellular exosome / extracellular region / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.1 Å | ||||||
Authors | Zhao, Y. / Ke, H. | ||||||
Citation | Journal: Biochemistry / Year: 1996 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cyh.cif.gz | 51.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cyh.ent.gz | 37.1 KB | Display | PDB format |
PDBx/mmJSON format | 5cyh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5cyh_validation.pdf.gz | 393.6 KB | Display | wwPDB validaton report |
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Full document | 5cyh_full_validation.pdf.gz | 394.5 KB | Display | |
Data in XML | 5cyh_validation.xml.gz | 5 KB | Display | |
Data in CIF | 5cyh_validation.cif.gz | 7.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/5cyh ftp://data.pdbj.org/pub/pdb/validation_reports/cy/5cyh | HTTPS FTP |
-Related structure data
-Links
-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.) Homo sapiens (human) / Cell line: XA90 / Gene: CYCLOPHILIN / Plasmid: PHN1+ / Gene (production host): CYCLOPHILIN / Production host: Escherichia coli (E. coli) / References: UniProt: P05092, UniProt: P62937*PLUS |
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#2: Chemical | ChemComp-GLY / |
#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: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.81 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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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 / Detector: IMAGE PLATE |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.1 Å / Num. obs: 8424 / % possible obs: 75 % / Redundancy: 4 % / Rmerge(I) obs: 0.062 |
Reflection | *PLUS % possible obs: 75.5 % / Num. measured all: 35845 |
Reflection shell | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 2.2 Å / % possible obs: 66 % |
-Processing
Software |
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Refinement | Resolution: 2.1→8 Å / σ(F): 2 /
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Displacement parameters | Biso mean: 27.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.175 / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |