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- PDB-6usy: COAGULATION FACTOR XI CATALYTIC DOMAIN (C123S) IN COMPLEX WITH NV... -

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Basic information

Entry
Database: PDB / ID: 6usy
TitleCOAGULATION FACTOR XI CATALYTIC DOMAIN (C123S) IN COMPLEX WITH NVP-XIV936
ComponentsCoagulation factor XIa light chain
KeywordsHYDROLASE / OTHER
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 / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family ...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 / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / 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-QGS / Coagulation factor XI
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.26 Å
AuthorsWeihofen, W.A. / Clark, K. / Nunes, S.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Structure-Based Design and Preclinical Characterization of Selective and Orally Bioavailable Factor XIa Inhibitors: Demonstrating the Power of an Integrated S1 Protease Family Approach.
Authors: Lorthiois, E. / Roache, J. / Barnes-Seeman, D. / Altmann, E. / Hassiepen, U. / Turner, G. / Duvadie, R. / Hornak, V. / Karki, R.G. / Schiering, N. / Weihofen, W.A. / Perruccio, F. / Calhoun, ...Authors: Lorthiois, E. / Roache, J. / Barnes-Seeman, D. / Altmann, E. / Hassiepen, U. / Turner, G. / Duvadie, R. / Hornak, V. / Karki, R.G. / Schiering, N. / Weihofen, W.A. / Perruccio, F. / Calhoun, A. / Fazal, T. / Dedic, D. / Durand, C. / Dussauge, S. / Fettis, K. / Tritsch, F. / Dentel, C. / Druet, A. / Liu, D. / Kirman, L. / Lachal, J. / Namoto, K. / Bevan, D. / Mo, R. / Monnet, G. / Muller, L. / Zessis, R. / Huang, X. / Lindsley, L. / Currie, T. / Chiu, Y.H. / Fridrich, C. / Delgado, P. / Wang, S. / Hollis-Symynkywicz, M. / Berghausen, J. / Williams, E. / Liu, H. / Liang, G. / Kim, H. / Hoffmann, P. / Hein, A. / Ramage, P. / D'Arcy, A. / Harlfinger, S. / Renatus, M. / Ruedisser, S. / Feldman, D. / Elliott, J. / Sedrani, R. / Maibaum, J. / Adams, C.M.
History
DepositionOct 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coagulation factor XIa light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3132
Polymers26,8561
Non-polymers4571
Water7,782432
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.950, 60.910, 67.300
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 XIa light chain / FXI / Plasma thromboplastin antecedent / PTA


Mass: 26856.496 Da / Num. of mol.: 1 / Mutation: C123S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F11 / Plasmid: pET / Details (production host): pET42a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03951, coagulation factor XIa
#2: Chemical ChemComp-QGS / 1-[(2S)-2-{3-[(3S)-3-amino-2,3-dihydro-1-benzofuran-5-yl]-5-(propan-2-yl)phenyl}-2-hydroxyethyl]-1H-indole-7-carboxylic acid


Mass: 456.533 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H28N2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 432 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.3 Å3/Da / Density % sol: 46.57 % / Description: orthorhombic
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Bit-Tris pH 7.0, 0.6 M NaCl, 25 % (w/v) PEG3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.26→18.27 Å / Num. obs: 66560 / % possible obs: 98.3 % / Observed criterion σ(I): 2.2 / Redundancy: 6.4 % / Biso Wilson estimate: 14.49 Å2 / Rsym value: 0.043 / Net I/σ(I): 19.3
Reflection shellResolution: 1.26→1.27 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.697 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2278 / % possible all: 95.8

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
BUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6R8X

6r8x


Resolution: 1.26→18.27 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.961 / SU R Cruickshank DPI: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.048 / SU Rfree Blow DPI: 0.049 / SU Rfree Cruickshank DPI: 0.045
RfactorNum. reflection% reflectionSelection details
Rfree0.188 3179 4.78 %RANDOM
Rwork0.166 ---
obs0.167 66458 98.2 %-
Displacement parametersBiso max: 81.32 Å2 / Biso mean: 19.62 Å2 / Biso min: 8.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.2233 Å20 Å20 Å2
2--0.1245 Å20 Å2
3---0.0988 Å2
Refine analyzeLuzzati coordinate error obs: 0.14 Å
Refinement stepCycle: final / Resolution: 1.26→18.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1875 0 34 433 2342
Biso mean--13.89 32.6 -
Num. residues----236
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d697SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes341HARMONIC5
X-RAY DIFFRACTIONt_it1999HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion258SEMIHARMONIC5
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_contact2671SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1999HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2728HARMONIC21.1
X-RAY DIFFRACTIONt_omega_torsion5.12
X-RAY DIFFRACTIONt_other_torsion13.97
LS refinement shellResolution: 1.26→1.26 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2459 69 5.19 %
Rwork0.2014 1261 -
all0.2036 1330 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 24.9176 Å / Origin y: -2.3271 Å / Origin z: -3.7239 Å
111213212223313233
T-0.0154 Å2-0.0025 Å20.0033 Å2--0.0156 Å2-0.0034 Å2---0.0272 Å2
L0.505 °2-0.2766 °2-0.0493 °2-0.8204 °2-0.1443 °2--0.3256 °2
S-0.0094 Å °-0.0298 Å °0.0215 Å °0.0294 Å °0.0281 Å °-0.0298 Å °-0.0389 Å °0.0004 Å °-0.0186 Å °
Refinement TLS groupSelection details: { A|* }

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