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- PDB-3hnb: Factor VIII Trp2313-His2315 segment is involved in membrane bindi... -

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Basic information

Entry
Database: PDB / ID: 3hnb
TitleFactor VIII Trp2313-His2315 segment is involved in membrane binding as shown by crystal structure of complex between factor VIII C2 domain and an inhibitor
ComponentsCoagulation factor VIII
KeywordsBLOOD CLOTTING / SMALL MOLECULE INHIBITOR/BLOOD CLOTTING
Function / homology
Function and homology information


Defective F8 accelerates dissociation of the A2 domain / Defective F8 binding to the cell membrane / Defective F8 secretion / Defective F8 sulfation at Y1699 / Gamma carboxylation, hypusinylation, hydroxylation, and arylsulfatase activation / Defective F8 binding to von Willebrand factor / blood coagulation, intrinsic pathway / Cargo concentration in the ER / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant ...Defective F8 accelerates dissociation of the A2 domain / Defective F8 binding to the cell membrane / Defective F8 secretion / Defective F8 sulfation at Y1699 / Gamma carboxylation, hypusinylation, hydroxylation, and arylsulfatase activation / Defective F8 binding to von Willebrand factor / blood coagulation, intrinsic pathway / Cargo concentration in the ER / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / COPII-coated ER to Golgi transport vesicle / COPII-mediated vesicle transport / Defective F8 cleavage by thrombin / Common Pathway of Fibrin Clot Formation / Intrinsic Pathway of Fibrin Clot Formation / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / acute-phase response / Golgi lumen / blood coagulation / Platelet degranulation / oxidoreductase activity / endoplasmic reticulum lumen / copper ion binding / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Coagulation factor 5/8-like / : / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / Multicopper oxidase, C-terminal / Multicopper oxidase ...Coagulation factor 5/8-like / : / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / Multicopper oxidase, C-terminal / Multicopper oxidase / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Multicopper oxidase, N-terminal / Multicopper oxidase / Galactose-binding domain-like / Cupredoxin / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-768 / Coagulation factor VIII
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsLiu, Z. / Yuan, C.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Trp2313-His2315 of factor VIII C2 domain is involved in membrane binding: structure of a complex between the C2 domain and an inhibitor of membrane binding.
Authors: Liu, Z. / Lin, L. / Yuan, C. / Nicolaes, G.A. / Chen, L. / Meehan, E.J. / Furie, B. / Furie, B. / Huang, M.
History
DepositionMay 31, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 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
M: Coagulation factor VIII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4932
Polymers18,0301
Non-polymers4631
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.054, 55.775, 67.971
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Coagulation factor VIII / recombine factor VIII / Procoagulant component / Antihemophilic factor / AHF


Mass: 18029.559 Da / Num. of mol.: 1
Fragment: C2 domain of Factor VIIIa light chain, UNP residues 2189-2347
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F8 / Plasmid: pPIC9K / Production host: pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: P00451
#2: Chemical ChemComp-768 / (2R)-1-(2,4-dichlorophenoxy)-3-[(2E)-2-imino-3-(2-piperidin-1-ylethyl)-2,3-dihydro-1H-benzimidazol-1-yl]propan-2-ol / 1-(2,4-dichlorophenoxy)-3-{2-imino-3-[2-(1-piperidinyl)ethyl]-2,3-dihydro-1H-benzimidazol-1-yl}-2-propanol


Mass: 463.400 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H28Cl2N4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.21 Å3/Da / Density % sol: 44.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2.8M sodium chloride, 0.1M Tris-HCl, 3% glycol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.04 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 30, 2008 / Details: mirrors
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 1.14→50 Å / Num. obs: 55023 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.084
Reflection shellResolution: 1.14→1.18 Å / % possible all: 76.8

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1D7P

1d7p


Resolution: 1.15→25.8 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 0.1 / SU B: 1.352 / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22 2791 5.1 %RANDOM
Rwork0.185 ---
all0.208 54940 --
obs0.187 54940 94.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 53.25 Å2 / Biso mean: 10.984 Å2 / Biso min: 3.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.15→25.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1243 0 31 167 1441
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0211506
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.9582080
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3535198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.69224.28663
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.09215257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.74157
X-RAY DIFFRACTIONr_chiral_restr0.0990.2220
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021202
X-RAY DIFFRACTIONr_nbd_refined0.2460.2705
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21053
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2139
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.231
X-RAY DIFFRACTIONr_mcbond_it1.0571.5932
X-RAY DIFFRACTIONr_mcangle_it1.50721514
X-RAY DIFFRACTIONr_scbond_it2.23668
X-RAY DIFFRACTIONr_scangle_it3.1164.5566
LS refinement shellResolution: 1.147→1.176 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 183 -
Rwork0.236 3421 -
all-3604 -
obs--85.34 %

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