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- PDB-5w06: HUMAN TISSUE FACTOR IN COMPLEX WITH ANTIBODY M1587 -

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Basic information

Entry
Database: PDB / ID: 5w06
TitleHUMAN TISSUE FACTOR IN COMPLEX WITH ANTIBODY M1587
Components
  • M1587 FAB HEAVY CHAIN
  • M1587 FAB LIGHT CHAIN
  • Tissue factor
KeywordsIMMUNE SYSTEM
Function / homology
Function and homology information


activation of plasma proteins involved in acute inflammatory response / activation of blood coagulation via clotting cascade / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway / NGF-stimulated transcription / cytokine receptor activity / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of endothelial cell apoptotic process / positive regulation of TOR signaling ...activation of plasma proteins involved in acute inflammatory response / activation of blood coagulation via clotting cascade / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway / NGF-stimulated transcription / cytokine receptor activity / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of endothelial cell apoptotic process / positive regulation of TOR signaling / positive regulation of endothelial cell proliferation / positive regulation of interleukin-8 production / protein processing / phospholipid binding / cytokine-mediated signaling pathway / positive regulation of angiogenesis / blood coagulation / : / protease binding / positive regulation of cell migration / external side of plasma membrane / positive regulation of gene expression / cell surface / extracellular space / membrane / plasma membrane
Similarity search - Function
Tissue factor / Tissue factor, conserved site / Tissue factor signature. / Interferon/interleukin receptor domain / Interferon-alpha/beta receptor, fibronectin type III / : / Tissue factor / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold ...Tissue factor / Tissue factor, conserved site / Tissue factor signature. / Interferon/interleukin receptor domain / Interferon-alpha/beta receptor, fibronectin type III / : / Tissue factor / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsTeplyakov, A. / Obmolova, G. / Malia, T.J. / Gilliland, G.L.
CitationJournal: MAbs / Year: 2018
Title: Structural insights into humanization of anti-tissue factor antibody 10H10.
Authors: Teplyakov, A. / Obmolova, G. / Malia, T.J. / Raghunathan, G. / Martinez, C. / Fransson, J. / Edwards, W. / Connor, J. / Husovsky, M. / Beck, H. / Chi, E. / Fenton, S. / Zhou, H. / Almagro, J.C. / Gilliland, G.L.
History
DepositionMay 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 4, 2023Group: 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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
T: Tissue factor
L: M1587 FAB LIGHT CHAIN
H: M1587 FAB HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,3974
Polymers73,3053
Non-polymers921
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-31 kcal/mol
Surface area29430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.100, 175.560, 63.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Tissue factor / TF / Coagulation factor III / Thromboplastin


Mass: 24560.229 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN (UNP residues 37-245)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F3 / Production host: Homo sapiens (human) / References: UniProt: P13726
#2: Antibody M1587 FAB LIGHT CHAIN


Mass: 24189.873 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Antibody M1587 FAB HEAVY CHAIN


Mass: 24554.551 Da / Num. of mol.: 1 / Fragment: FD
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#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.: 107 / 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: 2.61 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M SODIUM ACETATE PH 4.5, 18% PEG 3K, 0.2 M AMMONIUM ACETATE
PH range: 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 17, 2010 / Details: SI(111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 23936 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 41.1 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 16
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 1678 / % possible all: 94.7

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
REFMAC5.8.0135refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1uj3, 4m7k

1uj3

4m7k


Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.909 / SU B: 10.034 / SU ML: 0.211 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.652 / ESU R Free: 0.291
RfactorNum. reflection% reflectionSelection details
Rfree0.23495 954 4 %RANDOM
Rwork0.18625 ---
obs0.18822 22930 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.23 Å20 Å2-0 Å2
2---0.53 Å20 Å2
3---1.76 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4900 0 6 107 5013
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.025034
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1421.9516851
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1095.04632
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.35424.752202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.57315813
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6941516
X-RAY DIFFRACTIONr_chiral_restr0.0720.2770
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213757
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_it3.4465.5322529
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.55612.4063153
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.9555.7922504
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined9.8926934
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.603→2.669 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 65 -
Rwork0.269 1575 -
obs--94.6 %

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