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- PDB-7v10: Factor XIa in Complex with Compound 2d -

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Basic information

Entry
Database: PDB / ID: 7v10
TitleFactor XIa in Complex with Compound 2d
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-OQI / Coagulation factor XI
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.798 Å
AuthorsShaffer, P.L. / Spurlino, J. / Milligan, C.M.
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 1.3Oct 16, 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)27,6243
Polymers26,8561
Non-polymers7672
Water1,71195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.411, 59.693, 67.154
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-OQI / methyl ~{N}-[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]phenyl]carbamate


Mass: 574.993 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H24ClFN8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.22 Å3/Da / Density % sol: 44.52 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Aug 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.798→50 Å / Num. obs: 20090 / % possible obs: 88 % / Redundancy: 4 % / Biso Wilson estimate: 17.69 Å2 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.076 / Rrim(I) all: 0.161 / Χ2: 2.343 / Net I/σ(I): 7.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.798-1.833.20.997940.5240.6421.1851.2271.6
1.83-1.863.20.9788250.520.6311.1681.24972.9
1.86-1.93.30.7888180.6490.50.9361.2474.6
1.9-1.943.20.6578460.6630.4230.7841.28975.9
1.94-1.983.30.5568850.7530.3550.6621.32177.6
1.98-2.033.30.4418930.7850.280.5241.33880.3
2.03-2.083.30.3699210.8360.2340.4381.43281.2
2.08-2.133.30.3369560.8690.2120.3991.49983.9
2.13-2.23.40.2899640.890.1810.3411.4385.5
2.2-2.273.40.2819670.890.1760.3321.60987
2.27-2.353.50.25210360.9150.1560.2981.79391.1
2.35-2.443.70.24410690.9370.1460.2861.69893.6
2.44-2.553.80.22610730.9450.1330.2631.92294.6
2.55-2.6940.20210890.9550.1140.2332.0495.7
2.69-2.864.40.18211160.9640.0970.2072.18297.6
2.86-3.084.80.14811360.9770.0760.1672.51398.5
3.08-3.395.30.11911270.9840.0570.1323.17898.1
3.39-3.885.80.09711540.9910.0450.1073.63798.9
3.88-4.885.50.08211750.9920.040.0913.77598.6
4.88-504.70.08212460.9930.0420.0933.71898.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.1refinement
PDB_EXTRACT3.27data extraction
PHENIX1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SOS

3sos


Resolution: 1.798→44.615 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.23 1998 9.96 %
Rwork0.1902 18059 -
obs0.1942 20057 87.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.11 Å2 / Biso mean: 21.9915 Å2 / Biso min: 6.98 Å2
Refinement stepCycle: final / Resolution: 1.798→44.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1875 0 83 95 2053
Biso mean--25.64 24.58 -
Num. residues----236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072015
X-RAY DIFFRACTIONf_angle_d0.9332742
X-RAY DIFFRACTIONf_chiral_restr0.059284
X-RAY DIFFRACTIONf_plane_restr0.005360
X-RAY DIFFRACTIONf_dihedral_angle_d15.9451175
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7982-1.84320.34071070.293101871
1.8432-1.89310.3431190.2785105674
1.8931-1.94880.30131290.2385110776
1.9488-2.01170.31651230.2149114579
2.0117-2.08360.26251320.2006117581
2.0836-2.1670.23481380.1871121984
2.167-2.26560.2441310.1946125587
2.2656-2.3850.22221470.1979135292
2.385-2.53450.25281500.201137094
2.5345-2.73010.25861590.2018141696
2.7301-3.00480.26481580.2083144598
3.0048-3.43950.20141620.183145699
3.4395-4.33280.18911680.1521147799
4.3328-44.6150.18921750.1717156899
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)
12.11620.3140.09592.1866-0.15031.6347-0.0229-0.1366-0.16520.11890.0070.12830.1590.00540.01190.11690.01010.01610.08850.00560.1089-23.3208-15.489613.3017
24.224-0.20411.25672.58340.65771.3009-0.02950.00570.5537-0.0210.1029-0.0172-0.28420.1797-0.08840.2109-0.01090.03440.1158-0.02440.1655-20.16251.758615.5772
32.29620.3145-1.57280.37360.12453.56850.0684-0.2906-0.06020.10570.0132-0.23560.01120.4113-0.07030.14240.0102-0.0530.1596-0.02860.1768-5.4537-8.917812.897
42.132-0.03730.0681.9753-0.14421.93710.0208-0.09150.08280.06890.0843-0.2015-0.09950.2128-0.05050.0837-0.00880.0040.0944-0.03220.1098-11.7973-4.614411.3255
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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