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Open data
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Basic information
Entry | Database: PDB / ID: 4dgd | ||||||
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Title | TRIMCyp cyclophilin domain from Macaca mulatta: H70C mutant | ||||||
![]() | TRIMCyp | ||||||
![]() | ISOMERASE / anti-viral protein | ||||||
Function / homology | ![]() negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / heparan sulfate binding / regulation of viral genome replication / leukocyte chemotaxis / endothelial cell activation / negative regulation of stress-activated MAPK cascade / cyclosporin A binding / protein peptidyl-prolyl isomerization ...negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / heparan sulfate binding / regulation of viral genome replication / leukocyte chemotaxis / endothelial cell activation / negative regulation of stress-activated MAPK cascade / cyclosporin A binding / protein peptidyl-prolyl isomerization / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of protein dephosphorylation / activation of protein kinase B activity / neutrophil chemotaxis / negative regulation of protein phosphorylation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / negative regulation of protein kinase activity / platelet activation / platelet aggregation / integrin binding / protein folding / positive regulation of NF-kappaB transcription factor activity / cellular response to oxidative stress / positive regulation of MAPK cascade / response to hypoxia / protein ubiquitination / positive regulation of protein phosphorylation / intracellular membrane-bounded organelle / apoptotic process / zinc ion binding / extracellular region / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Caines, M.E.C. / Bichel, K. / Price, A.J. / McEwan, W.A. / James, L.C. | ||||||
![]() | ![]() Title: Diverse HIV viruses are targeted by a conformationally dynamic antiviral. Authors: Caines, M.E. / Bichel, K. / Price, A.J. / McEwan, W.A. / Towers, G.J. / Willett, B.J. / Freund, S.M. / James, L.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87.3 KB | Display | ![]() |
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PDB format | ![]() | 64.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 427.6 KB | Display | ![]() |
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Full document | ![]() | 427.7 KB | Display | |
Data in XML | ![]() | 10.5 KB | Display | |
Data in CIF | ![]() | 15.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4dgaC ![]() 4dgbC ![]() 4dgcC ![]() 4dgeC ![]() 2wlwS C: citing same article ( 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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Unit cell |
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Components
#1: Protein | Mass: 17981.469 Da / Num. of mol.: 1 / Fragment: cyclophilin domain (UNP residues 304-468) / Mutation: H70C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: B0LJC8, UniProt: P62940*PLUS, peptidylprolyl isomerase |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.6 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop Details: 25% w/v PEG4000, 8% v/v propan-2-ol, 0.1 M sodium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 11, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.4→43.924 Å / Num. all: 28507 / Num. obs: 28507 / % possible obs: 97.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 8.98 Å2 / Rsym value: 0.075 / Net I/σ(I): 10.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2WLW Resolution: 1.4→43.92 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.166 / WRfactor Rwork: 0.1341 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.922 / SU B: 1.848 / SU ML: 0.033 / SU R Cruickshank DPI: 0.0689 / SU Rfree: 0.0585 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 52.37 Å2 / Biso mean: 10.5434 Å2 / Biso min: 3.53 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→43.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
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