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- PDB-6x0t: Structure of human plasma factor XIIa in complex with (2S)-1-(N,3... -

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Entry
Database: PDB / ID: 6x0t
TitleStructure of human plasma factor XIIa in complex with (2S)-1-(N,3-dicyclohexyl-D-alanyl)-4-[(4R,5S)-4-methyl-5-phenyl-4,5-dihydro-1,3-oxazol-2-yl]-N-[(thiophen-2-yl)methyl]piperazine-2-carboxamide (compound 8h)
ComponentsCoagulation factor XII
KeywordsBLOOD CLOTTING / Protease / inhibitor
Function / homology
Function and homology information


coagulation factor XIIa / plasma kallikrein-kinin cascade / Factor XII activation / Defective SERPING1 causes hereditary angioedema / response to misfolded protein / positive regulation of plasminogen activation / blood coagulation, intrinsic pathway / misfolded protein binding / positive regulation of fibrinolysis / zymogen activation ...coagulation factor XIIa / plasma kallikrein-kinin cascade / Factor XII activation / Defective SERPING1 causes hereditary angioedema / response to misfolded protein / positive regulation of plasminogen activation / blood coagulation, intrinsic pathway / misfolded protein binding / positive regulation of fibrinolysis / zymogen activation / Defective factor XII causes hereditary angioedema / protein autoprocessing / positive regulation of blood coagulation / rough endoplasmic reticulum / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / protein processing / blood coagulation / collagen-containing extracellular matrix / serine-type endopeptidase activity / innate immune response / calcium ion binding / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Coagulation factor XII/hepatocyte growth factor activator / Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. ...Coagulation factor XII/hepatocyte growth factor activator / Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / EGF-like domain / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / : / Epidermal growth factor-like domain. / Kringle-like fold / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Chem-UJ7 / Coagulation factor XII
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.388 Å
AuthorsOrth, P.
CitationJournal: To Be Published
Title: Structure of human plasma factor XIIa in complex with (2S)-1-(N,3-dicyclohexyl-D-alanyl)-4-[(4R,5S)-4-methyl-5-phenyl-4,5-dihydro-1,3-oxazol-2-yl]-N-[(thiophen-2-yl)methyl]piperazine-2-carboxamide (compound 8h)
Authors: Rao, A.U. / Chu, H.D.
History
DepositionMay 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coagulation factor XII
B: Coagulation factor XII
C: Coagulation factor XII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,7657
Polymers83,8103
Non-polymers1,9564
Water5,459303
1
A: Coagulation factor XII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6523
Polymers27,9371
Non-polymers7162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Coagulation factor XII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5562
Polymers27,9371
Non-polymers6201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Coagulation factor XII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5562
Polymers27,9371
Non-polymers6201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.121, 133.413, 88.858
Angle α, β, γ (deg.)90, 104.4, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Coagulation factor XII / Hageman factor / HAF


Mass: 27936.568 Da / Num. of mol.: 3 / Fragment: UNP residues 357-615 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00748, coagulation factor XIIa
#2: Chemical ChemComp-UJ7 / (2S)-1-(N,3-dicyclohexyl-D-alanyl)-4-[(4R,5S)-4-methyl-5-phenyl-4,5-dihydro-1,3-oxazol-2-yl]-N-[(thiophen-2-yl)methyl]piperazine-2-carboxamide


Mass: 619.860 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C35H49N5O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.64 Å3/Da / Density % sol: 53.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 18% PEG3350, 200 mM lithium sulfate, 0.7 mM cadmium chloride, 100 mM Bis-Tris, pH 6.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 19, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.388→47.258 Å / Num. obs: 112839 / % possible obs: 92.4 % / Redundancy: 3.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.094 / Net I/σ(I): 6.6
Reflection shellResolution: 1.388→1.52 Å / Num. unique obs: 5643 / CC1/2: 0.568

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Processing

Software
NameVersionClassification
BUSTER2.11.7 (6-FEB-2020)refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
STARANISOdata scaling
autoBUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDb entry 2WUB

2wub


Resolution: 1.388→47.26 Å / Cor.coef. Fo:Fc: 0.851 / Cor.coef. Fo:Fc free: 0.833 / SU R Cruickshank DPI: 0.12 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.118 / SU Rfree Blow DPI: 0.113 / SU Rfree Cruickshank DPI: 0.115
RfactorNum. reflection% reflectionSelection details
Rfree0.3112 2229 -RANDOM
Rwork0.2889 ---
obs0.2893 110904 63.5 %-
Displacement parametersBiso mean: 10.82 Å2
Baniso -1Baniso -2Baniso -3
1--2.1895 Å20 Å20.2019 Å2
2---1.9698 Å20 Å2
3---4.1593 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: LAST / Resolution: 1.388→47.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5379 0 137 303 5819
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0085685HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.057766HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1796SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes975HARMONIC5
X-RAY DIFFRACTIONt_it5685HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion688SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4986SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.7
X-RAY DIFFRACTIONt_other_torsion16.18
LS refinement shellResolution: 1.39→1.47 Å
RfactorNum. reflection% reflection
Rfree0.1723 41 -
Rwork0.1973 --
obs0.1968 2219 7.82 %

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