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- PDB-4y7b: Factor Xa complex with GTC000441 -

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Basic information

Entry
Database: PDB / ID: 4y7b
TitleFactor Xa complex with GTC000441
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 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 / Laminin / Laminin / Coagulation Factor Xa inhibitory site / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. ...Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla domain superfamily / Laminin / Laminin / Coagulation Factor Xa inhibitory site / 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 family, serine active site. / Serine proteases, trypsin domain profile. / 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-44I / Coagulation factor X
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
Model detailsChains A & B are disulfide bonded together
AuthorsConvery, M.A. / Young, R.J. / Senger, S. / Hamblin, J.N. / Chan, C. / Toomey, J.R. / Watson, N.S.
Citation
#1: Journal: J. Med. Chem. / Year: 2007
Title: Factor Xa inhibitors: S1 binding interactions of a series of N-{(3S)-1-[(1S)-1-methyl-2-morpholin-4-yl-2-oxoethyl]-2-oxopyrrolidin-3-yl}sulfonamides.
Authors: Chan, C. / Borthwick, A.D. / Brown, D. / Burns-Kurtis, C.L. / Campbell, M. / Chaudry, L. / Chung, C.W. / Convery, M.A. / Hamblin, J.N. / Johnstone, L. / Kelly, H.A. / Kleanthous, S. / ...Authors: Chan, C. / Borthwick, A.D. / Brown, D. / Burns-Kurtis, C.L. / Campbell, M. / Chaudry, L. / Chung, C.W. / Convery, M.A. / Hamblin, J.N. / Johnstone, L. / Kelly, H.A. / Kleanthous, S. / Patikis, A. / Patel, C. / Pateman, A.J. / Senger, S. / Shah, G.P. / Toomey, J.R. / Watson, N.S. / Weston, H.E. / Whitworth, C. / Young, R.J. / Zhou, P.
History
DepositionFeb 13, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,3644
Polymers43,7612
Non-polymers6022
Water5,891327
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-23 kcal/mol
Surface area13820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.742, 72.635, 79.862
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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 / Details: Disulphide linked to other chain / 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: UNP residues 46-179 / Source method: isolated from a natural source / Details: Disulphide linked to other chain / Source: (natural) Homo sapiens (human) / 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-44I / 6-chloro-N-{(3S)-1-[(2S)-1-{(1R,5S)-7-[2-(methylamino)ethyl]-3,7-diazabicyclo[3.3.1]non-3-yl}-1-oxopropan-2-yl]-2-oxopy rrolidin-3-yl}naphthalene-2-sulfonamide / GTC000441


Mass: 562.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H36ClN5O4S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.88 Å3/Da / Density % sol: 34.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.75
Details: 18% PEG 6000, 100 mM MES PH 5.75, 10 mM calcium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 28, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.79→28.56 Å / Num. obs: 29751 / % possible obs: 99 % / Redundancy: 4 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 12.4
Reflection shellResolution: 1.8→1.87 Å / Rmerge(I) obs: 0.514

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Processing

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

1ezq


Resolution: 1.79→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.424 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2124 1578 5 %RANDOM
Rwork0.1739 ---
obs0.1758 29751 98.78 %-
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: 89.07 Å2 / Biso mean: 24.345 Å2 / Biso min: 10.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å20 Å2
2---1.29 Å20 Å2
3---0.72 Å2
Refinement stepCycle: final / Resolution: 1.79→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2235 0 39 327 2601
Biso mean--24.41 32.89 -
Num. residues----287
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192359
X-RAY DIFFRACTIONr_angle_refined_deg1.3121.9313191
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7565293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.78524.112107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.8615398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.561515
X-RAY DIFFRACTIONr_chiral_restr0.1020.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211786
LS refinement shellResolution: 1.792→1.838 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 79 -
Rwork0.257 1775 -
all-1854 -
obs--85.67 %

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