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- PDB-2fda: Crystal Structure of the Catalytic Domain of Human Coagulation Fa... -

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Basic information

Entry
Database: PDB / ID: 2fda
TitleCrystal Structure of the Catalytic Domain of Human Coagulation Factor XIa in Complex with alpha-Ketothiazole Arginine Derived Ligand
ComponentsCoagulation factor XI
KeywordsHYDROLASE / FXIa / Inhibitor
Function / homology
Function and homology information


coagulation factor XIa / serine-type aminopeptidase activity / Defective F9 activation / positive regulation of fibrinolysis / plasminogen activation / Intrinsic Pathway of Fibrin Clot Formation / blood coagulation / heparin binding / serine-type endopeptidase activity / extracellular space ...coagulation factor XIa / serine-type aminopeptidase activity / Defective F9 activation / positive regulation of fibrinolysis / plasminogen activation / Intrinsic Pathway of Fibrin Clot Formation / blood coagulation / heparin binding / serine-type endopeptidase activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Apple domain. / Apple domain / APPLE domain / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family ...Apple domain. / Apple domain / APPLE domain / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-682 / BICARBONATE ION / Coagulation factor XI
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsJin, L. / Pandey, P. / Babine, R.E. / Weaver, D.T. / Abdel-Meguid, S.S. / Strickler, J.E.
Citation
Journal: Bioorg.Med.Chem.Lett. / Year: 2006
Title: Synthesis, SAR exploration, and X-ray crystal structures of factor XIa inhibitors containing an alpha-ketothiazole arginine
Authors: Deng, H. / Bannister, T.D. / Jin, L. / Babine, R.E. / Quinn, J. / Nagafuji, P. / Celatka, C.A. / Lin, J. / Lazarova, T.I. / Rynkiewicz, M.J. / Bibbins, F. / Pandey, P. / Gorga, J. / Meyers, ...Authors: Deng, H. / Bannister, T.D. / Jin, L. / Babine, R.E. / Quinn, J. / Nagafuji, P. / Celatka, C.A. / Lin, J. / Lazarova, T.I. / Rynkiewicz, M.J. / Bibbins, F. / Pandey, P. / Gorga, J. / Meyers, H.V. / Abdel-Meguid, S.S. / Strickler, J.E.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Mutation of Surface Residues to Promote Crystallization of Activated Factor Xi as a Complex with Benzamidine: An Essential Step for the Iterative Structure-Based Design of Factor Xi Inhibitors
Authors: Jin, L. / Pandey, P. / Babine, R.E. / Weaver, D.T. / Abdel-Meguid, S.S. / Strickler, J.E.
History
DepositionDec 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coagulation factor XI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3565
Polymers26,7521
Non-polymers6044
Water4,594255
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.318, 121.318, 121.318
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Coagulation factor XI


Mass: 26752.369 Da / Num. of mol.: 1 / Fragment: light chain, catalytic domain, residues 388-625 / Mutation: S75A, K78A, T115A, C123S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F11 / Production host: Pichia pastoris (fungus) / Strain (production host): X-33 / References: UniProt: P03951, coagulation factor XIa
#2: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-682 / N~2~-(AMINOCARBONYL)-N~1~-{4-{[AMINO(IMINO)METHYL]AMINO}-1-[HYDROXY(1,3-THIAZOL-2-YL)METHYL]BUTYL}VALINAMIDE


Mass: 385.485 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H27N7O3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.78 Å3/Da / Density % sol: 55.76 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2.0 M AMMONIUM SULFATE, 0.1 M TRIS-HCL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 16, 2002 / Details: Blue Osmic Mirrors
RadiationMonochromator: Blue Osmic Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→28.6 Å / Num. all: 20224 / Num. obs: 20224 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 29.8
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 5.9 / Num. unique all: 1997 / % possible all: 100

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Processing

Software
NameVersionClassification
CNX2005refinement
HKL-2000data reduction
HKL-2000data scaling
CNX2005phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1ZHR

1zhr


Resolution: 2→28.6 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 369696.48 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1951 9.8 %RANDOM
Rwork0.186 ---
all-20224 --
obs-19908 98.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.3825 Å2 / ksol: 0.360468 e/Å3
Displacement parametersBiso mean: 27 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20 Å2
2---0.26 Å20 Å2
3---0.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2→28.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1891 0 39 255 2185
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.68
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.191.5
X-RAY DIFFRACTIONc_mcangle_it1.842
X-RAY DIFFRACTIONc_scbond_it1.912
X-RAY DIFFRACTIONc_scangle_it2.92.5
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.238 203 10.5 %
Rwork0.216 1727 -
obs-1989 96 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.parprotein.top
X-RAY DIFFRACTION2water_rep.parwater_rep.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4lig.parlig.top
X-RAY DIFFRACTION5covl.parcovl.top

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