coagulation factor VIIa / response to Thyroid stimulating hormone / response to 2,3,7,8-tetrachlorodibenzodioxine / response to astaxanthin / response to thyrotropin-releasing hormone / response to genistein / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway / response to vitamin K / response to carbon dioxide ...coagulation factor VIIa / response to Thyroid stimulating hormone / response to 2,3,7,8-tetrachlorodibenzodioxine / response to astaxanthin / response to thyrotropin-releasing hormone / response to genistein / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway / response to vitamin K / response to carbon dioxide / response to thyroxine / response to cholesterol / response to growth hormone / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of leukocyte chemotaxis / positive regulation of TOR signaling / positive regulation of blood coagulation / animal organ regeneration / 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 / serine-type peptidase activity / BMAL1:CLOCK,NPAS2 activates circadian gene expression / protein processing / Golgi lumen / circadian rhythm / response to estrogen / blood coagulation / response to estradiol / collagen-containing extracellular matrix / vesicle / response to hypoxia / positive regulation of cell migration / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / calcium ion binding / extracellular space / extracellular region / plasma membrane Similarity search - Function
DES-GLA FACTOR VIIA ... , 2 types, 4 molecules HILM
#1: Protein
DES-GLAFACTORVIIA (HEAVYCHAIN)
Mass: 28103.256 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Organ: LIVER / Plasmid: PCMV5 / Cell line (production host): HUMAN KIDNEY CELL LINE 293 / Production host: Homo sapiens (human) / References: UniProt: P08709, coagulation factor VIIa
#2: Protein
DES-GLAFACTORVIIA (LIGHTCHAIN)
Mass: 10994.179 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Organ: LIVER / Plasmid: PCMV5 / Cell line (production host): HUMAN KIDNEY CELL LINE 293 / Production host: Homo sapiens (human) / References: UniProt: P08709, coagulation factor VIIa
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Protein/peptide , 1 types, 2 molecules XY
#3: Protein/peptide
PEPTIDEE-76
Mass: 2198.461 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: Peptide E-76 was synthesized on a solid support, then cleaved and purified
Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
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Details
Nonpolymer details
THE INHIBITOR IS BOUND TO THE ACTIVE SITE OF THE ENZYME. THE UNBOUND FORM OF THE INHIBITOR IS D-PHE- ...THE INHIBITOR IS BOUND TO THE ACTIVE SITE OF THE ENZYME. THE UNBOUND FORM OF THE INHIBITOR IS D-PHE-PHE-ARG-CHLOROMETHYLKETONE. UPON REACTION WITH PROTEIN IT FORMS TWO COVALENT BONDS: 1) A COVALENT BOND TO SER 195 FORMING A HEMIKETAL AR7 AND 2) A COVALENT BOND TO NE2 OF HIS 57
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.57 Å3/Da / Density % sol: 52.18 %
Crystal grow
Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: PEG4000, t-butanol, sodium cacodylate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution: 3→3.16 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2478 / % possible all: 98.4
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 99 %
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Processing
Software
Name
Version
Classification
MOSFLM
datareduction
TRUNCATE
datareduction
AMoRE
phasing
X-PLOR
3.851
refinement
CCP4
(TRUNCATE)
datascaling
Refinement
Resolution: 3→50 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.2 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: BULK SOLVENT MODEL WAS APPLIED THERE IS UNPUBLISHED EXPERIMENTAL EVIDENCE THAT THE CARBOHYDRATE ATTACHED TO CHAINS L AND M DIFFERS FROM THAT DESCRIBED IN THIS ENTRY. SER 52 CARRIES 2 OR 3 ...Details: BULK SOLVENT MODEL WAS APPLIED THERE IS UNPUBLISHED EXPERIMENTAL EVIDENCE THAT THE CARBOHYDRATE ATTACHED TO CHAINS L AND M DIFFERS FROM THAT DESCRIBED IN THIS ENTRY. SER 52 CARRIES 2 OR 3 GLUCOSE RESIDUES, AND SER 60 CARRIES ALPHA-L-FUCOSE. THE ELECTRON DENSITY IN THIS REGION IS IMPERFECT, AND WAS FIT WITHOUT THIS INFORMATION. THE FIT IS ONLY MODERATELY SUCCESFUL.
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