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- PDB-4a7i: Factor Xa in complex with a potent 2-amino-ethane sulfonamide inh... -

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Basic information

Entry
Database: PDB / ID: 4a7i
TitleFactor Xa in complex with a potent 2-amino-ethane sulfonamide inhibitor
Components
  • ACTIVATED FACTOR XA HEAVY CHAIN XA
  • FACTOR X LIGHT CHAIN
KeywordsHYDROLASE / BLOOD COAGULATION FACTOR / CALCIUM- BINDING / EGF-LIKE DOMAIN / GAMMA-CARBOXYGLUTAMIC ACID / GLYCOPROTEIN / HYDROXYLATION / SERINE PROTEINASE / SERINE PROTEASE
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 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 ...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 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
Peptidase S1A, coagulation factor VII/IX/X/C/Z / Coagulation factor-like, Gla domain superfamily / Coagulation Factor Xa inhibitory site / Laminin / Laminin / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. ...Peptidase S1A, coagulation factor VII/IX/X/C/Z / Coagulation factor-like, Gla domain superfamily / Coagulation Factor Xa inhibitory site / Laminin / Laminin / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Ribbon / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-A7I / Coagulation factor X
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsNazare, M. / Matter, H. / Will, D.W. / Wagner, M. / Urmann, M. / Czech, J. / Schreuder, H. / Bauer, A. / Ritter, K. / Wehner, V.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2012
Title: Fragment Deconstruction of Small, Potent Factor Xa Inhibitors: Exploring the Superadditivity Energetics of Fragment Linking in Protein-Ligand Complexes.
Authors: Nazare, M. / Matter, H. / Will, D.W. / Wagner, M. / Urmann, M. / Czech, J. / Schreuder, H. / Bauer, A. / Ritter, K. / Wehner, V.
History
DepositionNov 14, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Remark 700 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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FACTOR X LIGHT CHAIN
B: ACTIVATED FACTOR XA HEAVY CHAIN XA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5184
Polymers39,0842
Non-polymers4342
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-21.7 kcal/mol
Surface area13220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.253, 72.042, 77.416
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein FACTOR X LIGHT CHAIN / / FACTOR XA / COAGULATION FACTOR X / STUART FACTOR / STUART-PROWER FACTOR


Mass: 10533.713 Da / Num. of mol.: 1 / Fragment: DES-GLA FACTOR X LIGHT CHAIN, RESIDUES 84-179 / Source method: isolated from a natural source / Details: MADE DES-GLA BY CHYMOTRYPSIN CLEAVAGE / Source: (natural) HOMO SAPIENS (human) / Tissue: BLOOD / References: UniProt: P00742, coagulation factor Xa
#2: Protein ACTIVATED FACTOR XA HEAVY CHAIN XA / FACTOR XA / COAGULATION FACTOR X / STUART FACTOR / STUART-PROWER FACTOR


Mass: 28550.596 Da / Num. of mol.: 1 / Fragment: ACTIVATED FACTOR X HEAVY CHAIN, RESIDUES 235-488 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Tissue: BLOOD / References: UniProt: P00742, coagulation factor Xa
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-A7I / 5-CHLORO-THIOPHENE-2-CARBOXYLIC ACID [2-(1--ISOPROPYL-PIPERIDIN-4-YLSULFAMOYL)-ETHYL]-AMIDE


Mass: 393.952 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24ClN3O3S2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.7 % / Description: NONE
Crystal growpH: 5.7
Details: PROTEIN SOLUTION: 8 MG/ML PROTEIN, 5 MM MES (PH 5.7), 5 MM CACL2, 100 MM BENZAMIDINE. RESERVOIR: 18-20% PEG-600, 50 MM MES (PH 5.7). SOAKING: ADD 10 MM INHIBITOR.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: May 2, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.4→19.66 Å / Num. obs: 12692 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 45.9 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 21
Reflection shellResolution: 2.4→2.48 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 6 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS2002refinement
XDSdata reduction
XSCALEdata scaling
CNXRIGID BODY REFINEMENTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: UNPUBLISHED FACTOR XA STRUCTURE

Resolution: 2.4→200 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELYHOOD
Details: DISORDERED SIDE CHAINS WERE MODELED STEREOCHEMICALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.253 618 4.8 %RANDOM
Rwork0.198 ---
obs0.198 12692 99.1 %-
Solvent computationSolvent model: MASK / Bsol: 51.4384 Å2 / ksol: 0.366996 e/Å3
Displacement parametersBiso mean: 46.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.102 Å20 Å20 Å2
2--0.276 Å20 Å2
3----0.378 Å2
Refinement stepCycle: LAST / Resolution: 2.4→200 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2247 0 25 206 2478
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004679
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.32328
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.7571.5
X-RAY DIFFRACTIONc_mcangle_it2.3162
X-RAY DIFFRACTIONc_scbond_it3.0212
X-RAY DIFFRACTIONc_scangle_it3.5712.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4A23.PARA23.PAR

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