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- PDB-35uj: Crystal structure of TFPI K2 domain in complex with 4D8 Fab fragment -

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Basic information

Entry
Database: PDB / ID: 35uj
TitleCrystal structure of TFPI K2 domain in complex with 4D8 Fab fragment
Components
  • 4D8 Heavy chain
  • 4D8 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: 2.9 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

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Assembly

Deposited unit
H: 4D8 Heavy chain
L: 4D8 Light chain
T: Tissue factor pathway inhibitor


Theoretical massNumber of molelcules
Total (without water)55,1633
Polymers55,1633
Non-polymers00
Water88349
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.102, 82.284, 103.628
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody 4D8 Heavy chain


Mass: 23590.320 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 4D8 Light chain


Mass: 23575.232 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
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: 2.4 Å3/Da / Density % sol: 48.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 12 % PEG 8000, 100 mM magnesium acetate, 100 mM MOPS pH 7.5

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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 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→43.85 Å / Num. obs: 12275 / % possible obs: 99.85 % / Redundancy: 5.77 % / Rmerge(I) obs: 0.124 / Rrim(I) all: 0.14 / Net I/σ(I): 4.47
Reflection shellResolution: 2.9→3.18 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.48 / Num. unique obs: 2872 / Rrim(I) all: 0.53 / % possible all: 99.85

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Processing

Software
NameVersionClassification
BUSTER2.11.1refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→43.85 Å / Cor.coef. Fo:Fc: 0.9413 / Cor.coef. Fo:Fc free: 0.8876 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.388
RfactorNum. reflection% reflectionSelection details
Rfree0.2424 586 4.77 %RANDOM
Rwork0.1707 ---
obs0.1741 12275 99.85 %-
Displacement parametersBiso mean: 59.98 Å2
Baniso -1Baniso -2Baniso -3
1--4.2502 Å20 Å20 Å2
2--0.8589 Å20 Å2
3---3.3913 Å2
Refine analyzeLuzzati coordinate error obs: 0.345 Å
Refinement stepCycle: LAST / Resolution: 2.9→43.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3726 0 0 49 3775
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013827HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.265204HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1269SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes89HARMONIC2
X-RAY DIFFRACTIONt_gen_planes552HARMONIC5
X-RAY DIFFRACTIONt_it3827HARMONIC20
X-RAY DIFFRACTIONt_chiral_improper_torsion503SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4198SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.3
X-RAY DIFFRACTIONt_other_torsion20.37
LS refinement shellResolution: 2.9→3.18 Å
RfactorNum. reflection% reflection
Rfree0.3036 140 4.87 %
Rwork0.1908 2732 -
obs--99.85 %
Refinement TLS params.

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)
13.33081.2652.42854.06072.9132.18540.06020.1495-0.04090.1495-0.101-0.2503-0.0409-0.25030.0408-0.0154-0.00170.0207-0.06820.0081-0.099333.519830.261856.836
20.9140.24130.84050.90620.92691.9652-0.0376-0.19690.063-0.1969-0.05230.02780.0630.02780.09-0.00220.02050.0096-0.1077-0.0179-0.074519.19919.429728.0321
31.63990.28081.97080.72381.37713.0132-0.2392-0.3462-0.6911-0.3462-0.224-0.3036-0.6911-0.30360.46310.09060.0772-0.1236-0.1172-0.0171-0.017612.744225.202221.8803
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ T|* }
2X-RAY DIFFRACTION2{ H|* }
3X-RAY DIFFRACTION3{ L|* }

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