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- PDB-8epk: Complex of anticoagulant RNA aptamer and human coagulation factor... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8epk | ||||||
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Title | Complex of anticoagulant RNA aptamer and human coagulation factor IXa (S195A) | ||||||
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![]() | BLOOD CLOTTING / coagulation factor IX / RNA aptamer / inhibitor | ||||||
Function / homology | ![]() Defective F9 secretion / Defective gamma-carboxylation of F9 / coagulation factor IXa / Defective F9 activation / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / zymogen activation / Extrinsic Pathway of Fibrin Clot Formation / Protein hydroxylation ...Defective F9 secretion / Defective gamma-carboxylation of F9 / coagulation factor IXa / Defective F9 activation / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / zymogen activation / Extrinsic Pathway of Fibrin Clot Formation / Protein hydroxylation / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Removal of aminoterminal propeptides from gamma-carboxylated proteins / Intrinsic Pathway of Fibrin Clot Formation / Golgi lumen / blood coagulation / collagen-containing extracellular matrix / endopeptidase activity / endoplasmic reticulum lumen / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular exosome / extracellular region / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Kolyadko, V.N. / Krishnaswamy, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Allosteric Control of Coagulation Factor IXa via Its Exosite II Regulates Blood Clotting Authors: Kolyadko, V.N. / Layzer, J.M. / Perry, K. / Sullenger, B.A. / Krishnaswamy, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 318.6 KB | Display | ![]() |
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PDB format | ![]() | 262.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 29.5 KB | Display | |
Data in CIF | ![]() | 38.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8epcC ![]() 8ephSC ![]() 3dd2S C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Coagulation factor IXa ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 7267.338 Da / Num. of mol.: 2 / Fragment: furin cleavage site (RRKR) inserted Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein | Mass: 26174.818 Da / Num. of mol.: 2 / Mutation: S195A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-RNA chain , 1 types, 2 molecules EF
#3: RNA chain | Mass: 10120.267 Da / Num. of mol.: 2 Fragment: 30 RNA residues with 2'-F and 2'-OMe modifications, capped with 5'-hexylamino linker and 3'-inverted deoxy-Thymidine residue (3'-3' linkage) Source method: obtained synthetically / Details: Chemically synthesized / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 3 types, 14 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
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![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 60 mM Na Citrate pH 5.0; 4% Tacsimate pH 7.0; 23% PEG 8000 PH range: 5.5 - 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 7, 2021 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.65→60.24 Å / Num. obs: 27106 / % possible obs: 98.5 % / Redundancy: 3.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.068 / Rrim(I) all: 0.128 / Net I/σ(I): 8.2 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 4
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8EPH, 3DD2 Resolution: 2.65→60.24 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.94 / SU B: 51.51 / SU ML: 0.427 / SU R Cruickshank DPI: 1.1256 / Cross valid method: THROUGHOUT / ESU R: 1.126 / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 171.79 Å2 / Biso mean: 93.716 Å2 / Biso min: 48.39 Å2
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Refinement step | Cycle: final / Resolution: 2.65→60.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.65→2.715 Å / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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