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- PDB-4dtg: Hemostatic effect of a monoclonal antibody mAb 2021 blocking the ... -

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Basic information

Entry
Database: PDB / ID: 4dtg
TitleHemostatic effect of a monoclonal antibody mAb 2021 blocking the interaction between FXa and TFPI in a rabbit hemophilia model
Components
  • (Humanized recombinant FAB fragment, FAB 2021, of a murine antibody, ...) x 2
  • Tissue factor pathway inhibitor
KeywordsBLOOD CLOTTING INHIBITOR/IMMUNE SYSTEM / antibody / inhibitor / blood coagulation / BLOOD CLOTTING INHIBITOR-IMMUNE SYSTEM complex
Function / homology
Function and homology information


negative regulation of blood coagulation / Extrinsic Pathway of Fibrin Clot Formation / cellular response to steroid hormone stimulus / endopeptidase inhibitor activity / side of membrane / serine-type endopeptidase inhibitor activity / caveola / blood coagulation / cell surface / endoplasmic reticulum ...negative regulation of blood coagulation / Extrinsic Pathway of Fibrin Clot Formation / cellular response to steroid hormone stimulus / endopeptidase inhibitor activity / side of membrane / serine-type endopeptidase inhibitor activity / caveola / blood coagulation / cell surface / endoplasmic reticulum / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Tissue factor pathway inhibitor-like / : / Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / 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. ...Tissue factor pathway inhibitor-like / : / Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / 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 / Few Secondary Structures / Irregular / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Tissue factor pathway inhibitor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSvensson, L.A. / Breinholt, J. / Krogh, B.O. / Hilden, I.
CitationJournal: Blood / Year: 2012
Title: Hemostatic effect of a monoclonal antibody mAb 2021 blocking the interaction between FXa and TFPI in a rabbit hemophilia model.
Authors: Hilden, I. / Lauritzen, B. / Sorensen, B.B. / Clausen, J.T. / Jespersgaard, C. / Krogh, B.O. / Bowler, A.N. / Breinholt, J. / Gruhler, A. / Svensson, L.A. / Petersen, H.H. / Petersen, L.C. / ...Authors: Hilden, I. / Lauritzen, B. / Sorensen, B.B. / Clausen, J.T. / Jespersgaard, C. / Krogh, B.O. / Bowler, A.N. / Breinholt, J. / Gruhler, A. / Svensson, L.A. / Petersen, H.H. / Petersen, L.C. / Balling, K.W. / Hansen, L. / Hermit, M.B. / Egebjerg, T. / Friederichsen, B. / Ezban, M. / Bjorn, S.E.
History
DepositionFeb 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Humanized recombinant FAB fragment, FAB 2021, of a murine antibody, light chain
H: Humanized recombinant FAB fragment, FAB 2021, of a murine antibody, heavy chain
K: Tissue factor pathway inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,09917
Polymers55,5323
Non-polymers1,56714
Water7,206400
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.010, 125.640, 202.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein , 1 types, 1 molecules K

#3: Protein Tissue factor pathway inhibitor / TFPI / Extrinsic pathway inhibitor / EPI / Lipoprotein-associated coagulation inhibitor / LACI


Mass: 7939.789 Da / Num. of mol.: 1
Fragment: Kunitz-type protease inhibitor domain 2 (UNP residues 119-178)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LACI, TFPI, TFPI (AMINO ACIDS 119-178), TFPI1 / Production host: Escherichia coli (E. coli) / References: UniProt: P10646

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Antibody , 2 types, 2 molecules LH

#1: Antibody Humanized recombinant FAB fragment, FAB 2021, of a murine antibody, light chain


Mass: 23846.619 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Cell line (production host): Human embryonic kidney 293 cells
Production host: Homo sapiens (human)
#2: Antibody Humanized recombinant FAB fragment, FAB 2021, of a murine antibody, heavy chain


Mass: 23745.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Cell line (production host): Human embryonic kidney 293 cells
Production host: Homo sapiens (human)

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Non-polymers , 4 types, 414 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 3.72 Å3/Da / Density % sol: 66.94 %
Crystal growTemperature: 295 K / pH: 6
Details: 0.05 M CALCIUM CHLORIDE, 0.1 M MES, pH 6.0, 45% V/V PEG 200, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 11, 2009 / Details: TWO MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR, SI(111). THE FIRST CRYSTAL IS WATER COOLED.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 76298 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 36 Å2 / Rsym value: 0.066 / Net I/σ(I): 12.7
Reflection shellResolution: 1.8→1.85 Å / Mean I/σ(I) obs: 2 / % possible all: 98.5

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.6.0119refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1F8T AND 1TFX

1f8t

1tfx


Resolution: 1.8→29.102 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.451 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23637 3817 5 %RANDOM
Rwork0.19585 ---
obs0.19789 72056 98.43 %-
all-77080 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.36 Å2
Baniso -1Baniso -2Baniso -3
1--12.23 Å20 Å20 Å2
2--17.85 Å20 Å2
3----5.62 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.102 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3827 0 102 400 4329
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.024128
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.6821.9755601
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7235535
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.73724.54174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.30615672
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3571520
X-RAY DIFFRACTIONr_chiral_restr0.1910.2622
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0213088
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 263 -
Rwork0.264 5130 -
obs--95.08 %
Refinement TLS params.

Method: refined / 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)
11.45630.64220.12040.96690.43421.50290.0492-0.2056-0.0410.1464-0.04980.02940.07140.05950.00050.28640.02320.01010.04280.04590.208317.47645.60716.936
21.29980.3342-0.00791.0415-0.17841.2521-0.0002-0.29080.00730.11990.01390.1196-0.027-0.1756-0.01370.40710.00620.01560.20860.1120.31712.17638.58349.595
33.20320.0810.4972.0402-0.63543.7253-0.04460.49860.1167-0.13140.0120.0163-0.040.07510.03260.247-0.00290.01670.07770.02130.199914.94848.541-7.876
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 113
2X-RAY DIFFRACTION1H1 - 122
3X-RAY DIFFRACTION2L114 - 219
4X-RAY DIFFRACTION2H123 - 221
5X-RAY DIFFRACTION3K2 - 61

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