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- PDB-2j95: CRYSTAL STRUCTURE OF A HUMAN FACTOR XA INHIBITOR COMPLEX -

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Basic information

Entry
Database: PDB / ID: 2j95
TitleCRYSTAL STRUCTURE OF A HUMAN FACTOR XA INHIBITOR COMPLEX
Components
  • ACTIVATED FACTOR XA HEAVY CHAIN
  • ACTIVATED FACTOR XA LIGHT CHAIN
KeywordsHYDROLASE / SERINE PROTEASE / EGF-LIKE DOMAIN / BLOOD COAGULATION / POLYMORPHISM / GLYCOPROTEIN / HYDROXYLATION / GAMMA- CARBOXYGLUTAMIC ACID / CALCIUM / ZYMOGEN / COMPLEX / 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-GSX / Coagulation factor X
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsChan, C. / Borthwick, A.D. / Brown, D. / Campbell, M. / Chaudry, L. / Chung, C.W. / Convery, M.A. / Hamblin, J.N. / Johnstone, L. / Kelly, H.A. ...Chan, C. / Borthwick, A.D. / Brown, D. / Campbell, M. / Chaudry, L. / Chung, C.W. / Convery, M.A. / Hamblin, J.N. / Johnstone, L. / Kelly, H.A. / Kleanthous, S. / Burns-Kurtis, C.L. / 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.
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
DepositionNov 2, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,3064
Polymers43,7612
Non-polymers5442
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)57.023, 73.024, 80.224
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 ACTIVATED FACTOR XA HEAVY CHAIN / STUART FACTOR / STUART-PROWER FACTOR


Mass: 28550.596 Da / Num. of mol.: 1 / Fragment: ACTIVATED DESGLA, RESIDUES 235-488 / Source method: isolated from a natural source
Details: PURCHASED FROM ENZYME RESEARCH LABS. ISOLATED FROM HUMAN BLOOD
Source: (natural) HOMO SAPIENS (human) / References: UniProt: P00742, coagulation factor Xa
#2: Protein ACTIVATED FACTOR XA LIGHT CHAIN / STUART FACTOR / STUART-PROWER FACTOR


Mass: 15210.793 Da / Num. of mol.: 1 / Fragment: ACTIVATED DESGLA, RESIDUES 46-179 / Source method: isolated from a natural source
Details: PURCHASED FROM ENZYME RESEARCH LABS. ISOLATED FROM HUMAN BLOOD
Source: (natural) HOMO SAPIENS (human) / References: UniProt: P00742, coagulation factor Xa
#3: Chemical ChemComp-GSX / 5'-CHLORO-N-{(3S)-1-[(1S)-1-METHYL-2-MORPHOLIN-4-YL-2-OXOETHYL]-2-OXOPYRROLIDIN-3-YL}-2,2'-BITHIOPHENE-5-SULFONAMIDE


Mass: 504.043 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H22ClN3O5S3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSOME RESIDUES IN CHAIN ARE NOT SEEN IN THE ELECTRON DENSITY. SEQUENCE DATABASE RESIDUES 1-45 (THE ...SOME RESIDUES IN CHAIN ARE NOT SEEN IN THE ELECTRON DENSITY. SEQUENCE DATABASE RESIDUES 1-45 (THE GLA DOMAIN) WERE BIOCHEMICALLY REMOVED IN CHAIN B SOME RESIDUES IN CHAIN ARE NOT SEEN IN THE ELECTRON DENSITY. SEQUENCE DATABASE RESIDUES 1-45 (THE GLA DOMAIN) WERE BIOCHEMICALLY REMOVED IN CHAIN B

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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: 2.45 Å3/Da / Density % sol: 35.53 %
Crystal growpH: 5.85 / Details: 18% PEG 6K, 100MM MES PH5.75, 10MM CACL2, pH 5.85

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: May 10, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 22752 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.05
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.38

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Processing

Software
NameVersionClassification
REFMAC5.3.0006refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EZQ

1ezq


Resolution: 2.01→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.524 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1154 5.1 %RANDOM
Rwork0.193 ---
obs0.195 21405 100 %-
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 mean: 36.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2---1.31 Å20 Å2
3---0.91 Å2
Refinement stepCycle: LAST / Resolution: 2.01→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2230 0 32 168 2430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222320
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.9613132
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9955284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.15924.112107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.99315394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7021515
X-RAY DIFFRACTIONr_chiral_restr0.1160.2333
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021760
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1950.2794
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21520
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2128
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.213
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0970.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.821492
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.96642264
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.7725999
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.3917868
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.01→2.06 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.311 88
Rwork0.239 1332

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