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- PDB-3k9x: X-ray crystal structure of human fxa in complex with (S)-N-((2-ME... -

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Basic information

Entry
Database: PDB / ID: 3k9x
TitleX-ray crystal structure of human fxa in complex with (S)-N-((2-METHYLBENZOFURAN-5-YLAMINO)(2-OXO-1-(2-OXO-2- (PYRROLIDIN-1-YL)ETHYL)AZEPAN-3- YLAMINO)METHYLENE)NICOTINAMIDE
Components(PROTEIN (Coagulation factor ...) x 2
KeywordsHYDROLASE / SERINE PROTEASE / EPIDERMAL GROWTH FACTOR LIKE DOMAIN / BLOOD COAGULATION FACTOR / CLEAVAGE ON PAIR OF BASIC RESIDUES / EGF-LIKE DOMAIN / GAMMA-CARBOXYGLUTAMIC ACID / GLYCOPROTEIN / HYDROXYLATION / ZYMOGEN / BLOOD CLOTTING / Blood coagulation / Disulfide bond / Protease / Secreted
Function / homology
Function and homology information


coagulation factor Xa / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of leukocyte chemotaxis / positive regulation of TOR signaling / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation ...coagulation factor Xa / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of leukocyte chemotaxis / positive regulation of TOR signaling / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / Intrinsic Pathway of Fibrin Clot Formation / phospholipid binding / Golgi lumen / blood coagulation / positive regulation of cell migration / endoplasmic reticulum lumen / external side of plasma membrane / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Peptidase S1A, coagulation factor VII/IX/X/C/Z / Coagulation factor-like, Gla domain superfamily / Laminin / Coagulation Factor Xa inhibitory site / Laminin / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. ...Peptidase S1A, coagulation factor VII/IX/X/C/Z / Coagulation factor-like, Gla domain superfamily / Laminin / Coagulation Factor Xa inhibitory site / Laminin / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Ribbon / 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 domain profile. / Serine proteases, trypsin family, serine active site. / 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-MBM / Coagulation factor X
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsKlei, H.E. / Kish, K. / Ghosh, K. / Rushith, A.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2009
Title: Aroylguanidine-based factor Xa inhibitors: the discovery of BMS-344577
Authors: Shi, Y. / Li, C. / O'Connor, S.P. / Zhang, J. / Shi, M. / Bisaha, S.N. / Wang, Y. / Sitkoff, D. / Pudzianowski, A.T. / Huang, C. / Klei, H.E. / Kish, K. / Yanchunas, J. / Liu, E.C. / Hartl, ...Authors: Shi, Y. / Li, C. / O'Connor, S.P. / Zhang, J. / Shi, M. / Bisaha, S.N. / Wang, Y. / Sitkoff, D. / Pudzianowski, A.T. / Huang, C. / Klei, H.E. / Kish, K. / Yanchunas, J. / Liu, E.C. / Hartl, K.S. / Seiler, S.M. / Steinbacher, T.E. / Schumacher, W.A. / Atwal, K.S. / Stein, P.D.
History
DepositionOct 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (Coagulation factor X)
B: PROTEIN (Coagulation factor X)
C: PROTEIN (Coagulation factor X)
D: PROTEIN (Coagulation factor X)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,88216
Polymers74,1704
Non-polymers1,71212
Water12,052669
1
A: PROTEIN (Coagulation factor X)
B: PROTEIN (Coagulation factor X)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,12510
Polymers37,0852
Non-polymers1,0408
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-36 kcal/mol
Surface area16030 Å2
MethodPISA
2
C: PROTEIN (Coagulation factor X)
D: PROTEIN (Coagulation factor X)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7576
Polymers37,0852
Non-polymers6724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-34 kcal/mol
Surface area15540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.263, 77.630, 73.732
Angle α, β, γ (deg.)90.000, 102.630, 90.000
Int Tables number4
Space group name H-MP1211
DetailsCHAINS A and C ARE EGF-LIKE DOMAINS. CHAINS B AND D ARE CATALYTIC DOMAINS.

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Components

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PROTEIN (Coagulation factor ... , 2 types, 4 molecules ACBD

#1: Protein PROTEIN (Coagulation factor X) / Stuart factor / Stuart-Prower factor / Factor X light chain / Factor X heavy chain / Activated ...Stuart factor / Stuart-Prower factor / Factor X light chain / Factor X heavy chain / Activated factor Xa heavy chain


Mass: 10213.346 Da / Num. of mol.: 2 / Fragment: EGF-LIKE DOMAINS (UNP residues 85 to 178) / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Secretion: BLOOD / References: UniProt: P00742, coagulation factor Xa
#2: Protein PROTEIN (Coagulation factor X) / Stuart factor / Stuart-Prower factor / Factor X light chain / Factor X heavy chain / Activated ...Stuart factor / Stuart-Prower factor / Factor X light chain / Factor X heavy chain / Activated factor Xa heavy chain


Mass: 26871.623 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAINS (UNP residues 235 to 472) / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Secretion: BLOOD / References: UniProt: P00742, coagulation factor Xa

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Non-polymers , 5 types, 681 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MBM / N-{N'-(2-methyl-1-benzofuran-5-yl)-N-[(3S)-2-oxo-1-(2-oxo-2-pyrrolidin-1-ylethyl)azepan-3-yl]carbamimidoyl}pyridine-3-carboxamide


Mass: 516.591 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H32N6O4
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 669 / 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: 2.34 Å3/Da / Density % sol: 47.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 15-22% W/V PEG MME 5000, 0.01 M CALCIUM ACETATE, 0.35 M SODIUM ACETATE, 0.1 M LITHIUM SULFATE, 0.1 M MES, pH 6.0, VAPOR DIFFUSION HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: BW7B / Wavelength: 0.8337 Å
DetectorType: MAR 345 / Detector: IMAGE PLATE / Date: Dec 6, 1998
RadiationProtocol: SINGLE WAVELENGTH DOSE MODE / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8337 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 51615 / % possible obs: 95.4 % / Rmerge(I) obs: 0.053 / Χ2: 0.923 / Net I/σ(I): 10.9
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.940.31433421.301192.3
1.94-1.990.2434120.995195.3
1.99-2.050.19434000.936195.3
2.05-2.110.14434240.933195.9
2.11-2.170.12634500.865195.8
2.17-2.250.10134240.902195.6
2.25-2.340.08934280.901196
2.34-2.450.08534710.97196.1
2.45-2.580.07434790.931196.7
2.58-2.740.06434790.964196.2
2.74-2.950.05734691.072196.4
2.95-3.250.04834821.052196.7
3.25-3.720.03234940.8196.3
3.72-4.680.02734440.57195
4.68-300.02534170.69192.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→28.538 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.25 / σ(F): 1.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.24 1000 1.94 %
Rwork0.176 --
obs0.177 51592 95.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.498 Å2 / ksol: 0.396 e/Å3
Displacement parametersBiso max: 80.8 Å2 / Biso mean: 28.37 Å2 / Biso min: 11.98 Å2
Baniso -1Baniso -2Baniso -3
1--6.858 Å2-0 Å2-1.233 Å2
2---3.529 Å20 Å2
3----8.424 Å2
Refinement stepCycle: LAST / Resolution: 1.9→28.538 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4950 0 116 669 5735
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0225188
X-RAY DIFFRACTIONf_angle_d1.9156968
X-RAY DIFFRACTIONf_chiral_restr0.149741
X-RAY DIFFRACTIONf_plane_restr0.01907
X-RAY DIFFRACTIONf_dihedral_angle_d18.6221911
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-20.2661400.1977087722794
2-2.1250.2791420.1777189733196
2.125-2.2890.2561430.1777242738596
2.289-2.520.2661440.1777250739496
2.52-2.8840.2611430.187301744496
2.884-3.6320.2481450.1667302744796
3.632-28.5420.1861430.177221736494

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