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- PDB-7ahv: Anti-FIXa Fab of mim8 in complex with human FIXa -

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Basic information

Entry
Database: PDB / ID: 7ahv
TitleAnti-FIXa Fab of mim8 in complex with human FIXa
Components
  • (Coagulation factor ...) x 2
  • (anti-FIXa Fab of mim8 ...) x 2
KeywordsBLOOD CLOTTING / Fab / anti-FIXa / hydrolase / mim8
Function / homology
Function and homology information


Defective F9 secretion / Defective gamma-carboxylation of F9 / coagulation factor IXa / Defective F9 activation / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / zymogen activation / Extrinsic Pathway of Fibrin Clot Formation / Protein hydroxylation ...Defective F9 secretion / Defective gamma-carboxylation of F9 / coagulation factor IXa / Defective F9 activation / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / zymogen activation / Extrinsic Pathway of Fibrin Clot Formation / Protein hydroxylation / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Removal of aminoterminal propeptides from gamma-carboxylated proteins / Intrinsic Pathway of Fibrin Clot Formation / Golgi lumen / blood coagulation / collagen-containing extracellular matrix / endopeptidase activity / endoplasmic reticulum lumen / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular exosome / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
Peptidase S1A, coagulation factor VII/IX/X/C/Z / Coagulation factor-like, Gla domain superfamily / Coagulation Factor Xa inhibitory site / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain ...Peptidase S1A, coagulation factor VII/IX/X/C/Z / Coagulation factor-like, Gla domain superfamily / Coagulation Factor Xa inhibitory site / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Chem-0GJ / Coagulation factor IX
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsJohansson, E.
CitationJournal: Blood / Year: 2021
Title: A factor VIIIa-mimetic bispecific antibody, Mim8, ameliorates bleeding upon severe vascular challenge in hemophilia A mice.
Authors: Ostergaard, H. / Lund, J. / Greisen, P.J. / Kjellev, S. / Henriksen, A. / Lorenzen, N. / Johansson, E. / Roder, G. / Rasch, M.G. / Johnsen, L.B. / Egebjerg, T. / Lund, S. / Rahbek-Nielsen, H. ...Authors: Ostergaard, H. / Lund, J. / Greisen, P.J. / Kjellev, S. / Henriksen, A. / Lorenzen, N. / Johansson, E. / Roder, G. / Rasch, M.G. / Johnsen, L.B. / Egebjerg, T. / Lund, S. / Rahbek-Nielsen, H. / Gandhi, P.S. / Lamberth, K. / Loftager, M. / Andersen, L.M. / Bonde, A.C. / Stavenuiter, F. / Madsen, D.E. / Li, X. / Holm, T.L. / Ley, C.D. / Thygesen, P. / Zhu, H. / Zhou, R. / Thorn, K. / Yang, Z. / Hermit, M.B. / Bjelke, J.R. / Hansen, B.G. / Hilden, I.
History
DepositionSep 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 20, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: anti-FIXa Fab of mim8 heavy chain
B: anti-FIXa Fab of mim8 light chain
L: Coagulation factor IX
H: Coagulation factor IX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,39123
Polymers80,3224
Non-polymers2,06919
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9440 Å2
ΔGint-272 kcal/mol
Surface area32650 Å2
Unit cell
Length a, b, c (Å)97.030, 97.030, 254.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Space group name HallP4w2c
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+3/4
#8: -y,-x,-z+1/4

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Components

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Coagulation factor ... , 2 types, 2 molecules LH

#3: Protein Coagulation factor IX / Christmas factor / Plasma thromboplastin component / PTC


Mass: 6470.354 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F9 / Production host: Escherichia coli (E. coli) / References: UniProt: P00740, coagulation factor IXa
#4: Protein Coagulation factor IX / Christmas factor / Plasma thromboplastin component / PTC


Mass: 26190.818 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F9 / Production host: Escherichia coli (E. coli) / References: UniProt: P00740, coagulation factor IXa

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Antibody , 2 types, 2 molecules AB

#1: Antibody anti-FIXa Fab of mim8 heavy chain


Mass: 24080.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK / Production host: Homo sapiens (human)
#2: Antibody anti-FIXa Fab of mim8 light chain


Mass: 23580.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 19 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-0GJ / L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide


Type: peptide-like / Mass: 395.862 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28ClN6O5
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

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Details

Has ligand of interestN

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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: 3.73 Å3/Da / Density % sol: 67.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 2 M ammonium sulphate, 0.1 M Hepes, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.105→48.52 Å / Num. obs: 22811 / % possible obs: 99.8 % / Redundancy: 13 % / Biso Wilson estimate: 50.79 Å2 / CC1/2: 0.957 / CC star: 0.989 / Rmerge(I) obs: 0.692 / Rpim(I) all: 0.1985 / Rrim(I) all: 0.7205 / Net I/σ(I): 4.3
Reflection shellResolution: 3.105→3.216 Å / Redundancy: 13 % / Rmerge(I) obs: 2.568 / Mean I/σ(I) obs: 0.95 / Num. unique obs: 28675 / CC1/2: 0.476 / CC star: 0.803 / Rpim(I) all: 0.7295 / Rrim(I) all: 2.672 / % possible all: 99.19

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Processing

Software
NameVersionClassification
PHENIXdev_3965refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PUB,3KCG

4pub

3kcg


Resolution: 3.11→48.52 Å / SU ML: 0.4551 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.4658
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2835 549 2.41 %
Rwork0.2269 22238 -
obs0.2283 22787 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.89 Å2
Refinement stepCycle: LAST / Resolution: 3.11→48.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5589 0 111 0 5700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01195808
X-RAY DIFFRACTIONf_angle_d1.67037885
X-RAY DIFFRACTIONf_chiral_restr0.0833862
X-RAY DIFFRACTIONf_plane_restr0.0106996
X-RAY DIFFRACTIONf_dihedral_angle_d7.5506791
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.11-3.420.36181340.3035388X-RAY DIFFRACTION99.53
3.42-3.910.3081350.25675472X-RAY DIFFRACTION99.88
3.91-4.930.24581360.18825552X-RAY DIFFRACTION99.98
4.93-48.520.26481440.20755826X-RAY DIFFRACTION99.98

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