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- PDB-35ui: Crystal structure of TFPI K2 domain in complex with TFPI-24 Fab f... -

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Basic information

Entry
Database: PDB / ID: 35ui
TitleCrystal structure of TFPI K2 domain in complex with TFPI-24 Fab fragment
Components
  • TFPI-24-Fab Heavy chain
  • TFPI-24-Fab light chain
  • Tissue factor pathway inhibitor
KeywordsBLOOD CLOTTING / Tissue factor pathway inhibitor / antibody / Fab fragment / TFPI / Kunitz domain / Factor Xa
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity / blood coagulation / :
Similarity search - Function
Tissue factor pathway inhibitor-like / : / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily
Similarity search - Domain/homology
Tissue factor pathway inhibitor
Similarity search - Component
Biological speciesHomo sapiens (human)
Macaca fascicularis (crab-eating macaque)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsJuo, Z.S. / Mosyak, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Discovery and optimization of marstacimab, a human monoclonal antibody targeting tissue factor pathway inhibitor for the treatment of hemophilia A and B
Authors: Jin, M. / Hett, S. / Jasuja, R. / Rakhe, S. / Narula, J. / Tam, A. / Apgar, J.R. / Juo, Z.S. / Mosyak, L. / Holsti, M. / Joyce, A. / Hurst, S. / Webster, R. / Lin, L. / Stahl, M. / Pittman, D.D. / Bloom, L.
History
DepositionMay 18, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: TFPI-24-Fab Heavy chain
L: TFPI-24-Fab light chain
T: Tissue factor pathway inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4004
Polymers54,3083
Non-polymers921
Water6,918384
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-33 kcal/mol
Surface area21800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.817, 71.362, 148.729
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody TFPI-24-Fab Heavy chain


Mass: 23199.994 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 TFPI-24-Fab light chain


Mass: 23109.670 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein Tissue factor pathway inhibitor


Mass: 7997.842 Da / Num. of mol.: 1 / Fragment: K2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca fascicularis (crab-eating macaque)
Production host: Homo sapiens (human) / References: UniProt: Q2PFV4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.09 Å3/Da / Density % sol: 41.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20 % PEG 3350, 200 mM ammonium nitrate

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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: Mar 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→28.96 Å / Num. obs: 46840 / % possible obs: 99.82 % / Redundancy: 5.76 % / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.06 / Net I/σ(I): 7.27
Reflection shellResolution: 1.75→1.79 Å / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 4.13 / Num. unique obs: 3428 / Rrim(I) all: 0.19 / % possible all: 99.82

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Processing

Software
NameVersionClassification
BUSTER2.11.1refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→28.96 Å / Cor.coef. Fo:Fc: 0.9414 / Cor.coef. Fo:Fc free: 0.9221 / SU R Cruickshank DPI: 0.119 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.126 / SU Rfree Blow DPI: 0.119 / SU Rfree Cruickshank DPI: 0.115
RfactorNum. reflection% reflectionSelection details
Rfree0.2269 2373 5.07 %RANDOM
Rwork0.19 ---
obs0.1919 46840 99.82 %-
Displacement parametersBiso mean: 30.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.0097 Å20 Å20 Å2
2--4.705 Å20 Å2
3----4.7146 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.75→28.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3569 0 6 384 3959
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013663HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.184986HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1202SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes76HARMONIC2
X-RAY DIFFRACTIONt_gen_planes532HARMONIC5
X-RAY DIFFRACTIONt_it3663HARMONIC20
X-RAY DIFFRACTIONt_chiral_improper_torsion481SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4284SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.94
X-RAY DIFFRACTIONt_other_torsion16.03
LS refinement shellResolution: 1.75→1.79 Å
RfactorNum. reflection% reflection
Rfree0.2106 177 5.16 %
Rwork0.2053 3251 -
obs--99.82 %

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