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- PDB-6aod: FXIa antibody complex -

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Basic information

Entry
Database: PDB / ID: 6aod
TitleFXIa antibody complex
Components
  • (FXIa Antibody FAB ...) x 2
  • Coagulation factor XI
KeywordsBLOOD CLOTTING/IMMUNE SYSTEM / FXIa Antibody FAB / BLOOD CLOTTING / BLOOD CLOTTING-IMMUNE SYSTEM 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 / 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 / Immunoglobulins / Peptidase S1, PA clan / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / Coagulation factor XI
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLolicato, M. / Minor, D.L.
CitationJournal: Structure / Year: 2018
Title: Structural Basis for Activity and Specificity of an Anticoagulant Anti-FXIa Monoclonal Antibody and a Reversal Agent.
Authors: Ely, L.K. / Lolicato, M. / David, T. / Lowe, K. / Kim, Y.C. / Samuel, D. / Bessette, P. / Garcia, J.L. / Mikita, T. / Minor, D.L. / Coughlin, S.R.
History
DepositionAug 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FXIa Antibody FAB Light Chain
B: FXIa Antibody FAB Heavy Chain
C: Coagulation factor XI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,67724
Polymers75,8123
Non-polymers1,86521
Water10,088560
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9600 Å2
ΔGint-114 kcal/mol
Surface area28490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.127, 136.127, 175.956
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11B-585-

HOH

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Components

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Protein , 1 types, 1 molecules C

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


Mass: 27874.590 Da / Num. of mol.: 1 / Fragment: UNP residues 388-624 / Mutation: N63Q, N104Q, C113S, S188A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F11 / Production host: Homo sapiens (human) / References: UniProt: P03951, coagulation factor XIa

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Antibody , 2 types, 2 molecules AB

#1: Antibody FXIa Antibody FAB Light Chain


Mass: 23270.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody FXIa Antibody FAB Heavy Chain


Mass: 24666.561 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 5 types, 581 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Co
#7: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 560 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.69 Å3/Da / Density % sol: 54.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 1.86 M ammonium sulfate, 8 mM CoCl2, 30 mM K/Na phosphate, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03316 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03316 Å / Relative weight: 1
ReflectionResolution: 1.8→107.98 Å / Num. obs: 76265 / % possible obs: 99 % / Redundancy: 8.9 % / Net I/σ(I): 13.99
Reflection shellHighest resolution: 1.8 Å / Rmerge(I) obs: 2.663 / CC1/2: 0.244

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDS1data scaling
Coot1model building
XDS1data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KMT

4kmt


Resolution: 1.8→107.9 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.175 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.107 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2068 3813 5 %RANDOM
Rwork0.18192 ---
obs0.18315 72436 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 37.237 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å20 Å2
2--0.44 Å20 Å2
3----0.88 Å2
Refinement stepCycle: 1 / Resolution: 1.8→107.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5059 0 102 560 5721
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0195309
X-RAY DIFFRACTIONr_bond_other_d0.0070.024769
X-RAY DIFFRACTIONr_angle_refined_deg2.0591.9567212
X-RAY DIFFRACTIONr_angle_other_deg1.1363.00211105
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4395.015667
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.83823.917217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.25915861
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0631527
X-RAY DIFFRACTIONr_chiral_restr0.1390.2796
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0215812
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021067
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.6493.3842628
X-RAY DIFFRACTIONr_mcbond_other3.6483.3832627
X-RAY DIFFRACTIONr_mcangle_it4.7225.0563282
X-RAY DIFFRACTIONr_mcangle_other4.7215.0573283
X-RAY DIFFRACTIONr_scbond_it5.7243.9832681
X-RAY DIFFRACTIONr_scbond_other5.7233.9832681
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.8165.7443923
X-RAY DIFFRACTIONr_long_range_B_refined10.1441.1625961
X-RAY DIFFRACTIONr_long_range_B_other10.14341.1715962
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.574 279 -
Rwork0.526 5301 -
obs--99.96 %

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