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- PDB-4d7f: Human FXIa in complex with small molecule inhibitors. -

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Basic information

Entry
Database: PDB / ID: 4d7f
TitleHuman FXIa in complex with small molecule inhibitors.
ComponentsCOAGULATION FACTOR XI
KeywordsHYDROLASE / SERINE PROTEASE
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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. ...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 / 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 / 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-IXA / Coagulation factor XI
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsSandmark, J. / Oster, L. / Jacso, T. / Ullah, V. / Redzick, A. / Borjesson, U. / Olsson, T. / Norberg, M. / Akerud, T.
CitationJournal: To be Published
Title: From Mm Fragments to Nm Compounds Using Iloe-NMR to Guide Linking of Compounds in Fragment Based Drug Discovery (Fbdd).
Authors: Jacso, T. / Ullah, V. / Sandmark, J. / Oster, L. / Redzick, A. / Borjesson, U. / Olsson, T. / Akerud, T.
History
DepositionNov 24, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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)27,6937
Polymers26,7521
Non-polymers9416
Water2,342130
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.293, 121.293, 121.293
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-1247-

SO4

21A-1247-

SO4

31A-2090-

HOH

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Components

#1: Protein COAGULATION FACTOR XI / FXI / PLASMA THROMBOPLASTIN ANTECEDENT / PTA / COAGULATION FACTOR XIA


Mass: 26752.369 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 388-625 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: KOMAGATAELLA PASTORIS (fungus) / References: UniProt: P03951, coagulation factor XIa
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-IXA / N-[(2S)-1-({4-[(diaminomethylidene)amino]butyl}amino)-1-oxo-3-phenylpropan-2-yl]-4-hydroxy-2-oxo-1,2-dihydroquinoline-6-carboxamide


Mass: 464.517 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H28N6O4
#4: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.78 Å3/Da / Density % sol: 55.74 % / Description: NONE
Crystal growpH: 8.5
Details: 2M AMMONIUM SULFATE, 0.1M TRIS-CL PH 8.5, 0.2M NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.62→85.8 Å / Num. obs: 37889 / % possible obs: 100 % / Observed criterion σ(I): 1.5 / Redundancy: 20 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 21.5
Reflection shellResolution: 1.62→1.71 Å / Redundancy: 19.3 % / Mean I/σ(I) obs: 1.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→85.77 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.156 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21054 1891 5 %RANDOM
Rwork0.18357 ---
obs0.18488 35978 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.993 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.62→85.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1868 0 60 130 2058
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191983
X-RAY DIFFRACTIONr_bond_other_d0.0060.021814
X-RAY DIFFRACTIONr_angle_refined_deg1.2361.962692
X-RAY DIFFRACTIONr_angle_other_deg0.71234173
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9855237
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.28923.63688
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0315329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3481513
X-RAY DIFFRACTIONr_chiral_restr0.0710.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022252
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02459
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_it1.573.418945
X-RAY DIFFRACTIONr_mcbond_other1.5663.414944
X-RAY DIFFRACTIONr_mcangle_it2.4475.1221180
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2663.851038
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
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: 1.618→1.66 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 142 -
Rwork0.345 2597 -
obs--99.42 %

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