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- PDB-3ens: Crystal structure of human FXA in complex with methyl (2Z)-3-[(3-... -

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Basic information

Entry
Database: PDB / ID: 3ens
TitleCrystal structure of human FXA in complex with methyl (2Z)-3-[(3-chloro-1H-indol-7-yl)amino]-2-cyano-3-{[(3S)-2-oxo-1-(2-oxo-2-pyrrolidin-1-ylethyl)azepan-3-yl]amino}acrylate
Components
  • Activated factor Xa heavy chain
  • Factor X light chain
KeywordsHYDROLASE / BLOOD CLOTTING / 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
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 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 ...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 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 / Coagulation Factor Xa inhibitory site / Laminin / Laminin / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / 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 / Coagulation Factor Xa inhibitory site / Laminin / Laminin / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / 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
ACETATE ION / methyl / Coagulation factor X
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKlei, H.E.
CitationJournal: J.Med.Chem. / Year: 2008
Title: Design, Structure-Activity Relationships, X-ray Crystal Structure, and Energetic Contributions of a Critical P1 Pharmacophore: 3-Chloroindole-7-yl-Based Factor Xa Inhibitors.
Authors: Shi, Y. / Sitkoff, D. / Zhang, J. / Klei, H.E. / Kish, K. / Liu, E.C. / Hartl, K.S. / Seiler, S.M. / Chang, M. / Huang, C. / Youssef, S. / Steinbacher, T.E. / Schumacher, W.A. / Grazier, N. ...Authors: Shi, Y. / Sitkoff, D. / Zhang, J. / Klei, H.E. / Kish, K. / Liu, E.C. / Hartl, K.S. / Seiler, S.M. / Chang, M. / Huang, C. / Youssef, S. / Steinbacher, T.E. / Schumacher, W.A. / Grazier, N. / Pudzianowski, A. / Apedo, A. / Discenza, L. / Yanchunas, J. / Stein, P.D. / Atwal, K.S.
History
DepositionSep 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 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: Factor X light chain
B: Activated factor Xa heavy chain
C: Factor X light chain
D: Activated factor Xa heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,47521
Polymers74,1704
Non-polymers2,30517
Water5,477304
1
A: Factor X light chain
B: Activated factor Xa heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,28411
Polymers37,0852
Non-polymers1,1999
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-33 kcal/mol
Surface area16470 Å2
MethodPISA
2
C: Factor X light chain
D: Activated factor Xa heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,19210
Polymers37,0852
Non-polymers1,1078
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-32 kcal/mol
Surface area16050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.311, 78.861, 73.850
Angle α, β, γ (deg.)90.00, 102.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Factor X light chain /


Mass: 10213.346 Da / Num. of mol.: 2 / Fragment: sequence database residues 93-178 / Source method: isolated from a natural source / Details: BLOOD / Source: (natural) Homo sapiens (human) / References: UniProt: P00742, coagulation factor Xa
#2: Protein Activated factor Xa heavy chain


Mass: 26871.623 Da / Num. of mol.: 2 / Fragment: sequence database residues 235-472 / Source method: isolated from a natural source / Details: BLOOD / Source: (natural) Homo sapiens (human) / References: UniProt: P00742, coagulation factor Xa

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Non-polymers , 7 types, 321 molecules

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


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ENS / methyl (2Z)-3-[(3-chloro-1H-indol-7-yl)amino]-2-cyano-3-{[(3S)-2-oxo-1-(2-oxo-2-pyrrolidin-1-ylethyl)azepan-3-yl]amino}acrylate / methyl (2Z)-3-[(3-chloro-1H-indol-7-yl)amino]-2-cyano-3-{[(3S)-2-oxo-1-(2-oxo-2-pyrrolidin-1-ylethyl)azepan-3-yl]amino}prop-2-enoate / Methyl group


Mass: 512.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H29ClN6O4
#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: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#8: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE PROTEIN, AS ISOLATED FROM HUMAN BLOOD BY ENZYME RESEARCH LABORATORIES (SOUTH BEND, IN), WAS ...THE PROTEIN, AS ISOLATED FROM HUMAN BLOOD BY ENZYME RESEARCH LABORATORIES (SOUTH BEND, IN), WAS FOUND TO BE HETEROGENEOUS BY MASS SPECTROMETRY. THE REPROTED SEQRES RECORDS INCLUDE THE RESIDUES CONSISTENT WITH THE CARBOXYPEPTIDASE B CLEAVAGE SITE TO FORM DES-GLA PROTEIN AND THE RESIDUES MODELED IN ELECTRON DENSITY. N-TERMINI OF LIGHT CHAINS (CHAINS A AND C) MODELED BASED ON 1XKA. THERE MAY BE MORE RESIDUES BEYOND THESE TERMINI.

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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: 2.44 Å3/Da / Density % sol: 49.66 %
Crystal growTemperature: 298 K / pH: 6.5
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 6.500000, VAPOR DIFFUSION HANGING DROP, temperature 298K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 9, 1999 / Details: OSMIC
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 30240 / % possible obs: 97.3 % / Rmerge(I) obs: 0.1
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 2.5 / % possible all: 94.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→19.029 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.43 / σ(F): 1.48 / Phase error: 28.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.286 1000 3.31 %
Rwork0.2228 --
obs0.225 30221 97.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.43 Å2 / ksol: 0.402 e/Å3
Displacement parametersBiso mean: 29.923 Å2
Baniso -1Baniso -2Baniso -3
1-5.9591 Å2-0 Å20.7248 Å2
2---5.0722 Å20 Å2
3----0.8869 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.029 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4978 0 150 304 5432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055237
X-RAY DIFFRACTIONf_angle_d0.9467018
X-RAY DIFFRACTIONf_dihedral_angle_d18.1121938
X-RAY DIFFRACTIONf_chiral_restr0.064740
X-RAY DIFFRACTIONf_plane_restr0.004907
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.4210.35731380.2554037X-RAY DIFFRACTION95
2.421-2.57240.32541400.25334101X-RAY DIFFRACTION96
2.5724-2.77040.30871420.2424128X-RAY DIFFRACTION97
2.7704-3.04820.33931420.24264170X-RAY DIFFRACTION97
3.0482-3.48690.27391440.21594217X-RAY DIFFRACTION98
3.4869-4.38430.24881460.18924237X-RAY DIFFRACTION99
4.3843-19.02920.24681480.20724331X-RAY DIFFRACTION99

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