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- PDB-1zsl: Factor XI complexed with a pyrimidinone inhibitor -

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Basic information

Entry
Database: PDB / ID: 1zsl
TitleFactor XI complexed with a pyrimidinone inhibitor
ComponentsCoagulation factor XI
KeywordsHYDROLASE / serine protease / coagulation / covalent complex
Function / homology
Function and homology information


coagulation factor XIa / serine-type aminopeptidase activity / Defective F9 activation / positive regulation of fibrinolysis / plasminogen activation / Intrinsic Pathway of Fibrin Clot Formation / blood coagulation / heparin binding / serine-type endopeptidase activity / extracellular space ...coagulation factor XIa / serine-type aminopeptidase activity / Defective F9 activation / positive regulation of fibrinolysis / plasminogen activation / Intrinsic Pathway of Fibrin Clot Formation / blood coagulation / heparin binding / serine-type endopeptidase activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Apple domain. / Apple domain / APPLE domain / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / 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. ...Apple domain. / Apple domain / APPLE domain / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / 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-624 / Coagulation factor XI
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.05 Å
AuthorsNagafuji, P. / Jin, L. / Rynkiewicz, M. / Quinn, J. / Bibbins, F. / Meyers, H. / Babine, R. / Strickler, J. / Abdel-Meguid, S.
CitationJournal: To be Published
Title: Pyrimidinone Inhibitors of a Thrombolytic Protease
Authors: Nagafuji, P. / Jin, L. / Rynkiewicz, M. / Quinn, J. / Bibbins, F. / Meyers, H. / Babine, R. / Strickler, J. / Abdel-Meguid, S.
History
DepositionMay 24, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coagulation factor XI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3782
Polymers26,7981
Non-polymers5801
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.385, 122.385, 122.385
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Coagulation factor XI / Plasma thromboplastin antecedent / PTA / FXI


Mass: 26798.395 Da / Num. of mol.: 1 / Fragment: Coagulation Factor XIa Light Chain / Mutation: K455A/C500S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F11 / Plasmid: pPICZa A / Production host: Pichia pastoris (fungus) / Strain (production host): X-33 / References: UniProt: P03951, coagulation factor XIa
#2: Chemical ChemComp-624 / 2-(2-(3,4-DICHLOROPHENYL)-5-(ISOPROPYLAMINO)-6-OXOPYRIMIDIN-1(6H)-YL)-N-((S)-1-OXO-1-(THIAZOL-2-YL)-5-GUANIDINOPENTAN-2-YL)ACETAMIDE


Mass: 579.502 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H28Cl2N8O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.86 Å3/Da / Density % sol: 56.73 %
Crystal growTemperature: 283 K / Method: vapor diffusion / pH: 7.6
Details: 20% PEGMME 5000, 0.2 M ammonium sulfate, 0.1 M tris, pH 7.6, VAPOR DIFFUSION, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 18, 2002 / Details: Osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 20714 / Num. obs: 20714 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 25 Å2
Reflection shellResolution: 2→2.05 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CNX2002refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNX2002phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb code 1ZHR Factor Xi complexed with benzamidine

1zhr


Resolution: 2.05→28.85 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2966495.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 983 5.1 %RANDOM
Rwork0.239 ---
all-19266 --
obs-19266 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.5938 Å2 / ksol: 0.342561 e/Å3
Displacement parametersBiso mean: 34.7 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.05→28.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1876 0 38 114 2028
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_improper_angle_d0.77
LS refinement shellResolution: 2.05→2.18 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.345 151 4.8 %
Rwork0.292 3008 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.pprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.parwater_rep.top
X-RAY DIFFRACTION4carbohydrate.carbohydrate.
X-RAY DIFFRACTION5624.par624.top

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