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- PDB-7v13: Factor XIa in Complex with Compound 2g -

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Basic information

Entry
Database: PDB / ID: 7v13
TitleFactor XIa in Complex with Compound 2g
ComponentsCoagulation factor XIa light chain
KeywordsBLOOD CLOTTING / Hydrolase / SERINE PROTEASE / COAGULATION FACTOR
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
CITRIC ACID / Chem-ORF / Coagulation factor XI
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.589 Å
AuthorsShaffer, P.L. / Milligan, C.M. / Cedervall, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2022
Title: Discovery of Potent and Orally Bioavailable Pyridine N-Oxide-Based Factor XIa Inhibitors through Exploiting Nonclassical Interactions.
Authors: Xu, G. / Liu, Z. / Wang, X. / Lu, T. / DesJarlais, R.L. / Thieu, T. / Zhang, J. / Devine, Z.H. / Du, F. / Li, Q. / Milligan, C.M. / Shaffer, P. / Cedervall, P.E. / Spurlino, J.C. / Stratton, ...Authors: Xu, G. / Liu, Z. / Wang, X. / Lu, T. / DesJarlais, R.L. / Thieu, T. / Zhang, J. / Devine, Z.H. / Du, F. / Li, Q. / Milligan, C.M. / Shaffer, P. / Cedervall, P.E. / Spurlino, J.C. / Stratton, C.F. / Pietrak, B. / Szewczuk, L.M. / Wong, V. / Steele, R.A. / Bruinzeel, W. / Chintala, M. / Silva, J. / Gaul, M.D. / Macielag, M.J. / Nargund, R.
History
DepositionMay 11, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 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)27,6043
Polymers26,8561
Non-polymers7472
Water2,540141
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.250, 59.510, 66.760
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: C500S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F11 / Production host: Komagataella pastoris (fungus) / References: UniProt: P03951, coagulation factor XIa
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-ORF / 3-chloranyl-4-[1-[(1~{R})-1-[5-[3-chloranyl-2-fluoranyl-6-(1,2,3,4-tetrazol-1-yl)phenyl]-1-oxidanyl-pyridin-2-yl]-2-cyclopropyl-ethyl]pyrazol-4-yl]-5-fluoranyl-pyridine


Mass: 555.366 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H18Cl2F2N8O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.19 Å3/Da / Density % sol: 43.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 24% PEG 4000, 100mM Na Citrate pH 5.0

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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: Nov 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.589→33.38 Å / Num. obs: 32390 / % possible obs: 99.7 % / Redundancy: 6.4 % / Biso Wilson estimate: 22.41 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.025 / Rrim(I) all: 0.062 / Χ2: 1.143 / Net I/σ(I): 15.9
Reflection shellResolution: 1.589→1.646 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.728 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3197 / CC1/2: 0.8 / Rpim(I) all: 0.328 / Rrim(I) all: 0.861 / % possible all: 99.35

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Processing

Software
NameVersionClassification
XDS20180409data reduction
XSCALE20180409data scaling
PHENIX1.13refinement
PDB_EXTRACT3.27data extraction
PHENIX1.13phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SOS

3sos


Resolution: 1.589→33.38 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1886 1527 4.72 %
Rwork0.1639 30865 -
obs0.165 32390 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.64 Å2 / Biso mean: 30.5363 Å2 / Biso min: 15.86 Å2
Refinement stepCycle: final / Resolution: 1.589→33.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1875 0 51 141 2067
Biso mean--28.84 39.08 -
Num. residues----236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052003
X-RAY DIFFRACTIONf_angle_d0.82729
X-RAY DIFFRACTIONf_plane_restr0.005357
X-RAY DIFFRACTIONf_chiral_restr0.057285
X-RAY DIFFRACTIONf_dihedral_angle_d16.2531168
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.589-1.64020.27361380.24622757100
1.6402-1.69890.23211460.2202275599
1.6989-1.76690.22821440.1962757100
1.7669-1.84730.22351220.17892793100
1.8473-1.94470.18751370.16422776100
1.9447-2.06650.17961490.15782773100
2.0665-2.2260.20351470.1642784100
2.226-2.450.18661310.17192806100
2.45-2.80440.21511550.17252819100
2.8044-3.53270.15991160.15722871100
3.5327-33.380.17161430.1483297499
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8247-0.2403-0.09842.12160.24841.6011-0.01250.05810.1407-0.0573-0.0180.1382-0.159-0.03470.03290.1832-0.0074-0.00810.17430.00250.1817-23.121315.3773-13.1768
25.13650.1717-1.04922.71250.73741.2686-0.1056-0.1479-0.63220.1930.11720.02470.31930.1242-0.06640.27880.0153-0.03120.19380.0040.22-19.9867-1.624-15.7483
32.2009-0.18781.59060.89820.56822.87850.01060.23460.0449-0.04590.0642-0.1819-0.05030.3185-0.08280.1838-0.01640.04040.2289-0.01780.2193-5.59828.8755-13.4143
42.66220.1684-0.27171.8657-0.04322.27130.03230.0285-0.0643-0.04390.0419-0.20160.11940.2513-0.06410.19030.0134-0.01990.1757-0.01670.1722-11.76484.3429-11.2186
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 388 through 491 )A388 - 491
2X-RAY DIFFRACTION2chain 'A' and (resid 492 through 518 )A492 - 518
3X-RAY DIFFRACTION3chain 'A' and (resid 519 through 557 )A519 - 557
4X-RAY DIFFRACTION4chain 'A' and (resid 558 through 623 )A558 - 623

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