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- PDB-4dgb: TRIMCyp cyclophilin domain from Macaca mulatta: HIV-2 CA cyclophi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4dgb | ||||||
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Title | TRIMCyp cyclophilin domain from Macaca mulatta: HIV-2 CA cyclophilin-binding loop complex | ||||||
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![]() | ISOMERASE/VIRAL PROTEIN / anti-viral protein / ISOMERASE-VIRAL PROTEIN complex | ||||||
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 / viral budding via host ESCRT complex ...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 / viral budding via host ESCRT complex / 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 / host multivesicular body / platelet aggregation / integrin binding / protein folding / positive regulation of NF-kappaB transcription factor activity / cellular response to oxidative stress / viral nucleocapsid / positive regulation of MAPK cascade / response to hypoxia / protein ubiquitination / positive regulation of protein phosphorylation / intracellular membrane-bounded organelle / apoptotic process / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / RNA binding / zinc ion binding / extracellular region / membrane / 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 | ![]() | 81 KB | Display | ![]() |
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PDB format | ![]() | 60 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.9 KB | Display | ![]() |
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Full document | ![]() | 426.6 KB | Display | |
Data in XML | ![]() | 10.7 KB | Display | |
Data in CIF | ![]() | 15.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4dgaC ![]() 4dgcC ![]() 4dgdC ![]() 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: 18016.473 Da / Num. of mol.: 1 / Fragment: cyclophilin domain (UNP residues 304-468) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: B0LJC8, UniProt: P62940*PLUS, peptidylprolyl isomerase |
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#2: Protein/peptide | Mass: 550.647 Da / Num. of mol.: 1 / Fragment: cyclophilin-binding loop (UNP residues 221-226) / Source method: obtained synthetically / Source: (synth.) ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 36.02 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.3 Details: 2.35 M ammonium phosphate dibasic, 0.1 M Tris-HCl, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 9, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.702→71.08 Å / Num. all: 16284 / Num. obs: 15839 / % possible obs: 95 % / Redundancy: 2.3 % / Biso Wilson estimate: 17.04 Å2 / Rsym value: 0.037 / Net I/σ(I): 14.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.702→30.34 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.2115 / WRfactor Rwork: 0.1775 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8878 / SU B: 3.89 / SU ML: 0.068 / SU R Cruickshank DPI: 0.128 / SU Rfree: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 56.33 Å2 / Biso mean: 18.2559 Å2 / Biso min: 9.58 Å2
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Refinement step | Cycle: LAST / Resolution: 1.702→30.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.702→1.746 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 9.3657 Å / Origin y: -0.2112 Å / Origin z: 7.0043 Å
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