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- PDB-4na7: Factor XIA in complex with the inhibitor 3'-[(2S,4R)-6-carbamimid... -

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Basic information

Entry
Database: PDB / ID: 4na7
TitleFactor XIA in complex with the inhibitor 3'-[(2S,4R)-6-carbamimidoyl-4-methyl-4-phenyl-1,2,3,4-tetrahydroquinolin-2-yl]-4-carbamoyl-5'-[(3-methylbutanoyl)amino]biphenyl-2-carboxylic acid
ComponentsCoagulation factor XIFactor XI
KeywordsHYDROLASE/HYDROLASE INHIBITOR / hydrolase / serine protease / blood coagulation factor / protein inhibitor complex / HYDROLASE-HYDROLASE INHIBITOR 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 / membrane / identical protein binding / 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 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-1T5 / Coagulation factor XI
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWei, A.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Tetrahydroquinoline Derivatives as Potent and Selective Factor XIa Inhibitors.
Authors: Quan, M.L. / Wong, P.C. / Wang, C. / Woerner, F. / Smallheer, J.M. / Barbera, F.A. / Bozarth, J.M. / Brown, R.L. / Harpel, M.R. / Luettgen, J.M. / Morin, P.E. / Peterson, T. / Ramamurthy, V. ...Authors: Quan, M.L. / Wong, P.C. / Wang, C. / Woerner, F. / Smallheer, J.M. / Barbera, F.A. / Bozarth, J.M. / Brown, R.L. / Harpel, M.R. / Luettgen, J.M. / Morin, P.E. / Peterson, T. / Ramamurthy, V. / Rendina, A.R. / Rossi, K.A. / Watson, C.A. / Wei, A. / Zhang, G. / Seiffert, D. / Wexler, R.R.
History
DepositionOct 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Database references
Revision 1.2Apr 3, 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 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)28,5935
Polymers27,7011
Non-polymers8924
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.249, 104.960, 143.998
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Coagulation factor XI / Factor XI / FXI / Plasma thromboplastin antecedent / PTA / Coagulation factor XIa heavy chain / Coagulation ...FXI / Plasma thromboplastin antecedent / PTA / Coagulation factor XIa heavy chain / Coagulation factor XIa light chain


Mass: 27701.443 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F11 / Plasmid: PET14B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03951, coagulation factor XIa
#2: Chemical ChemComp-1T5 / 3'-[(2S,4R)-6-carbamimidoyl-4-methyl-4-phenyl-1,2,3,4-tetrahydroquinolin-2-yl]-4-carbamoyl-5'-[(3-methylbutanoyl)amino]biphenyl-2-carboxylic acid


Mass: 603.710 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H37N5O4
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE STRUCTURE ALSO CONTAINS A PORTION OF THE HEAVY CHAIN THAT IS UNOBSERVED CORRESPONDING TO THE ...THE STRUCTURE ALSO CONTAINS A PORTION OF THE HEAVY CHAIN THAT IS UNOBSERVED CORRESPONDING TO THE SEQUENCE MDDDDKMDNECTTKIKPR. IT IS LINKED BY A DISULPHIDE BOND TO CYS 122

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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: 3.11 Å3/Da / Density % sol: 60.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 100 mM Sodium Acetate, pH 4.5, 25%(W/V) PEG 8000, 100 mM ammonium sulfate, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: May 18, 2004 / Details: MICROMAX CONFOCAL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 8645 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 60.69 Å2 / Rmerge(I) obs: 0.186 / Net I/σ(I): 11.7
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.721 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
BUSTER-TNTBUSTER 2.11.2refinement
PDB_EXTRACT3.11data extraction
HKL-2000(DENZO)data reduction
HKL-2000(SCALEPACK)data scaling
AMoREphasing
BUSTER2.11.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FACTOR XIA DOUBLE MUTANT

Resolution: 2.8→29.69 Å / Cor.coef. Fo:Fc: 0.8843 / Cor.coef. Fo:Fc free: 0.8389 / Occupancy max: 1 / Occupancy min: 0 / SU R Cruickshank DPI: 1.144 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.244 / SU Rfree Blow DPI: 0.358 / SU Rfree Cruickshank DPI: 0.358
RfactorNum. reflection% reflectionSelection details
Rfree0.2694 920 10.7 %RANDOM
Rwork0.2372 ---
obs0.2407 8602 99.63 %-
Displacement parametersBiso max: 87.85 Å2 / Biso mean: 19.0914 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--1.0683 Å20 Å20 Å2
2---1.8334 Å20 Å2
3---2.9017 Å2
Refine analyzeLuzzati coordinate error obs: 0.503 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1860 0 60 30 1950
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d669SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes43HARMONIC2
X-RAY DIFFRACTIONt_gen_planes341HARMONIC5
X-RAY DIFFRACTIONt_it2007HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion253SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2181SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2007HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2760HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion3.81
X-RAY DIFFRACTIONt_other_torsion18.63
LS refinement shellResolution: 2.8→3.13 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3814 253 10.61 %
Rwork0.3459 2131 -
all0.3499 2384 -
obs--99.63 %

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