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Open data
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Basic information
Entry | Database: PDB / ID: 2wpm | ||||||
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Title | factor IXa superactive mutant, EGR-CMK inhibited | ||||||
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![]() | BLOOD CLOTTING / SERINE PROTEASE / ZYMOGEN / HYDROLASE / GLYCOPROTEIN / HYDROXYLATION / PHOSPHOPROTEIN / SULFATION / HEMOSTASIS / HEMOPHILIA / XASE-LIKE VARIANT / COMMUNICATION CHANNEL / GAMMA-CARBOXYGLUTAMIC ACID / EGF-LIKE DOMAIN / DISEASE MUTATION | ||||||
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 | ![]() ![]() | ||||||
![]() | Zogg, T. / Brandstetter, H. | ||||||
![]() | ![]() Title: Structural Basis of the Cofactor- and Substrate-Assisted Activation of Human Coagulation Factor Ixa Authors: Zogg, T. / Brandstetter, H. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "SB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "SB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81.5 KB | Display | ![]() |
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PDB format | ![]() | 58 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443.8 KB | Display | ![]() |
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Full document | ![]() | 449.9 KB | Display | |
Data in XML | ![]() | 16.9 KB | Display | |
Data in CIF | ![]() | 24.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2wphSC ![]() 2wpiC ![]() 2wpjC ![]() 2wpkC ![]() 2wplC 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: 6496.395 Da / Num. of mol.: 1 / Fragment: EGF2 DOMAIN, RESIDUES 133-191 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 361.375 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
#3: Protein | Mass: 26068.672 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 227-461 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#4: Chemical | ChemComp-CA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.38 % / Description: NONE |
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Crystal grow | pH: 6.85 / Details: 22 % PEG 3000 100 MM BIS/TRIS PH 6.85 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 4, 2008 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→21.7 Å / Num. obs: 16727 / % possible obs: 83.6 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2 / % possible all: 68.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2WPH Resolution: 2→21.7 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Bsol: 51.99 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2→21.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.11 Å / Total num. of bins used: 10 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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