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- PDB-4y79: Factor Xa complex with GTC000406 -

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Basic information

Entry
Database: PDB / ID: 4y79
TitleFactor Xa complex with GTC000406
Components(Coagulation factor ...) 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-4O6 / Coagulation factor X
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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.
CitationJournal: 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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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)44,2685
Polymers43,7612
Non-polymers5063
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-32 kcal/mol
Surface area13700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.914, 72.756, 79.901
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Coagulation factor ... , 2 types, 2 molecules AB

#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: UNP residues 46-179 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00742, coagulation factor Xa

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Non-polymers , 4 types, 240 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-4O6 / (E)-2-(4-chlorophenyl)-N-{(3S)-1-[(2S)-1-(morpholin-4-yl)-1-oxopropan-2-yl]-2-oxopyrrolidin-3-yl}ethenesulfonamide / GTC000406


Mass: 441.929 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H24ClN3O5S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 1.89 Å3/Da / Density % sol: 34.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.75
Details: 18% PEG 6000, 100 mM MES PH5.75, 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: May 10, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→28.6 Å / Num. obs: 19640 / % possible obs: 99.05 % / Redundancy: 4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.414

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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: 2.1→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.426 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2161 1004 5.1 %RANDOM
Rwork0.1752 ---
obs0.1772 18635 99.05 %-
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: 98.34 Å2 / Biso mean: 33.704 Å2 / Biso min: 13.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20 Å20 Å2
2---1.47 Å20 Å2
3---0.67 Å2
Refinement stepCycle: final / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2235 0 31 237 2503
Biso mean--41.54 38.72 -
Num. residues----287
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192343
X-RAY DIFFRACTIONr_angle_refined_deg1.3911.9383160
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.675289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.43924.167108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.81215396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3731515
X-RAY DIFFRACTIONr_chiral_restr0.10.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211774
LS refinement shellResolution: 2.105→2.159 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 71 -
Rwork0.223 1091 -
all-1162 -
obs--90.22 %

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