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- PDB-4y6d: Factor Xa complex with GTC000101 -

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Basic information

Entry
Database: PDB / ID: 4y6d
TitleFactor Xa complex with GTC000101
Components(Coagulation factor X) x 2
KeywordsHYDROLASE / Inhibitor
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
Peptidase S1A, coagulation factor VII/IX/X/C/Z / Coagulation factor-like, Gla domain superfamily / Laminin / Coagulation Factor Xa inhibitory site / Laminin / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / 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 / Laminin / Coagulation Factor Xa inhibitory site / Laminin / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / 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-48U / Coagulation factor X
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
Model detailsChains A & B are disulfide bonded together
AuthorsConvery, M.A.
CitationJournal: To Be Published
Title: TBA
Authors: Convery, M.A.
History
DepositionFeb 12, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coagulation factor X
B: Coagulation factor X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2333
Polymers43,7612
Non-polymers4721
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-9 kcal/mol
Surface area13440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.863, 72.729, 78.586
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

#1: Protein Coagulation factor X / Stuart factor / Stuart-Prower factor / Activated factor Xa heavy chain


Mass: 28550.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00742, coagulation factor Xa
#2: Protein Coagulation factor X / Stuart factor / Stuart-Prower factor / Factor X light chain


Mass: 15210.793 Da / Num. of mol.: 1 / Fragment: FACTOR X LIGHT CHAIN, UNP residues 46-179 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00742, coagulation factor Xa
#3: Chemical ChemComp-48U / 4-[(3S)-3-({[(E)-2-(5-chlorothiophen-2-yl)ethenyl]sulfonyl}amino)-2-oxopyrrolidin-1-yl]-3-fluoro-N,N-dimethylbenzamide / GTC000101


Mass: 471.953 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H19ClFN3O4S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 1.86 Å3/Da / Density % sol: 33.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 16-20% PEG 6K, 50mM Mes-NaOH pH 5.7-6.0, 5 mM CaCl2, and 50 mM NaCl
PH range: 5.7-6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 8, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.55→25 Å / Num. obs: 46306 / % possible obs: 96.2 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.055 / Χ2: 0.984 / Net I/av σ(I): 18.983 / Net I/σ(I): 12.6 / Num. measured all: 157978
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-IDRejects% possible all
1.55-1.610.51439560.8131083.5
1.61-1.670.39245920.821096.6
1.67-1.750.25846140.8361097.4
1.75-1.840.18646440.8961097.2
1.84-1.950.12146360.9721097.5
1.95-2.10.08246821.0421097.7
2.1-2.310.06247071.0871098.1
2.31-2.650.0547491.1481098.2
2.65-3.340.04347781.1441098.1
3.34-250.0449481.0221097.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.15data extraction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ezq

1ezq


Resolution: 1.55→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.747 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2334 2342 5.1 %RANDOM
Rwork0.1985 43868 --
obs0.2002 43868 96.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 89.17 Å2 / Biso mean: 28.035 Å2 / Biso min: 10.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2---1.1 Å20 Å2
3---1.17 Å2
Refinement stepCycle: final / Resolution: 1.55→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2200 0 60 307 2567
Biso mean--33.17 38.47 -
Num. residues----282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022378
X-RAY DIFFRACTIONr_angle_refined_deg1.3441.9733232
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.945293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.27824.112107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.56915400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6491515
X-RAY DIFFRACTIONr_chiral_restr0.0950.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211842
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 138 -
Rwork0.28 2588 -
all-2726 -
obs--79.96 %

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