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- PDB-6r8x: COAGULATION FACTOR XI CATALYTIC DOMAIN IN COMPLEX WITH FAB-PORTIO... -

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Basic information

Entry
Database: PDB / ID: 6r8x
TitleCOAGULATION FACTOR XI CATALYTIC DOMAIN IN COMPLEX WITH FAB-PORTION OF MAA868
Components
  • Coagulation factor XIFactor XI
  • anti-Factor-XI Fab fragment heavy chain MAA868
  • anti-Factor-XI Fab fragment light chain MAA868
KeywordsBLOOD CLOTTING / Coagulation FXI / Zymogen / Antibody / Antagonist
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 / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Coagulation factor XI
Similarity search - Component
Biological speciesHomo sapiens (human)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsSchiering, N. / Koch, A.
CitationJournal: Blood / Year: 2019
Title: MAA868, a novel FXI antibody with a unique binding mode, shows durable effects on markers of anticoagulation in humans.
Authors: Koch, A.W. / Schiering, N. / Melkko, S. / Ewert, S. / Salter, J. / Zhang, Y. / McCormack, P. / Yu, J. / Huang, X. / Chiu, Y.H. / Chen, Z. / Schleeger, S. / Horny, G. / DiPetrillo, K. / ...Authors: Koch, A.W. / Schiering, N. / Melkko, S. / Ewert, S. / Salter, J. / Zhang, Y. / McCormack, P. / Yu, J. / Huang, X. / Chiu, Y.H. / Chen, Z. / Schleeger, S. / Horny, G. / DiPetrillo, K. / Muller, L. / Hein, A. / Villard, F. / Scharenberg, M. / Ramage, P. / Hassiepen, U. / Cote, S. / DeGagne, J. / Krantz, C. / Eder, J. / Stoll, B. / Kulmatycki, K. / Feldman, D.L. / Hoffmann, P. / Basson, C.T. / Frost, R.J.A. / Khder, Y.
History
DepositionApr 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coagulation factor XI
B: anti-Factor-XI Fab fragment light chain MAA868
C: anti-Factor-XI Fab fragment heavy chain MAA868


Theoretical massNumber of molelcules
Total (without water)74,7423
Polymers74,7423
Non-polymers00
Water7,440413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-33 kcal/mol
Surface area28890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.274, 53.216, 65.164
Angle α, β, γ (deg.)90.00, 94.56, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 26856.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03951, coagulation factor XIa
#2: Antibody anti-Factor-XI Fab fragment light chain MAA868


Mass: 22921.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Antibody anti-Factor-XI Fab fragment heavy chain MAA868


Mass: 24963.904 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 413 / Source method: isolated from a natural source / Formula: H2O

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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: 2.21 Å3/Da / Density % sol: 44.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 3350 9MG/ML SEEDING (ORIGINAL CRYSTAL FROM WHICH SEEDS WERE PREPARED GREW AFTER 3 WEEKS)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00002 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 2.04→64.96 Å / Num. obs: 40205 / % possible obs: 95.9 % / Redundancy: 3.22 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 10.87
Reflection shellResolution: 2.04→2.09 Å / Redundancy: 3.18 % / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 2.67 / % possible all: 98.4

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
BUSTER2.11.5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: fXI CD plus trucated Fab structures

Resolution: 2.04→64.9 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2822 --
Rwork0.2201 --
obs-40088 95.9 %
Refinement stepCycle: LAST / Resolution: 2.04→64.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5036 0 0 413 5449

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