- PDB-4btu: Factor Xa in complex with the dual thrombin-FXa inhibitor 57. -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4btu
Title
Factor Xa in complex with the dual thrombin-FXa inhibitor 57.
Components
COAGULATION FACTOR X HEAVY CHAIN
COAGULATION FACTOR X LIGHT CHAIN
Keywords
HYDROLASE / SAR107375 / FACTOR XA INHIBITOR / THROMBIN INHIBITOR / CHLOROTHIOPHENE P1 FRAGMENT / S3 SUBSITE / MICROSOMES STABILITY / ORAL ANTITHROMBOTIC / DUAL INHIBITOR / IV ANTITHROMBOTIC
Function / homology
Function and homology information
coagulation factor Xa / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of leukocyte chemotaxis / positive regulation of TOR signaling / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation ...coagulation factor Xa / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of leukocyte chemotaxis / positive regulation of TOR signaling / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / Intrinsic Pathway of Fibrin Clot Formation / phospholipid binding / Golgi lumen / blood coagulation / positive regulation of cell migration / endoplasmic reticulum lumen / external side of plasma membrane / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region / plasma membrane Similarity search - Function
SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BB" 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.
#209 - May 2017 Tissue Transglutaminase and Celiac Disease similarity (1)
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Assembly
Deposited unit
A: COAGULATION FACTOR X LIGHT CHAIN B: COAGULATION FACTOR X HEAVY CHAIN E: COAGULATION FACTOR X LIGHT CHAIN F: COAGULATION FACTOR X HEAVY CHAIN hetero molecules
Mass: 18.015 Da / Num. of mol.: 566 / Source method: isolated from a natural source / Formula: H2O
Sequence details
GLA DOMAIN REMOVED WITH CHYMOTRYPSIN
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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: 2.42 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal grow
Method: vapor diffusion, hanging drop / pH: 5.7 Details: PROTEIN SOLUTION: 8 MG/ML REMARK 280 DESGLA FACTOR XA, 5 MM MES (PH 6.0), 5 MM CACL2, 100 MM REMARK 280 BENZAMIDINE. RESERVOIR SOLUTION: 18-20% PEG600, 50 MM MES REMARK 280 (PH 5.7). HANGING DROP SETUP.
Method to determine structure: MOLECULAR REPLACEMENT Starting model: IN-HOUSE FACTOR XA STRUCTURE Resolution: 2.37→46.51 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.891 / SU B: 7.656 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.24761
1117
4.6 %
RANDOM
Rwork
0.16932
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obs
0.17284
23315
99.96 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK