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- PDB-3hpt: Crystal structure of human FxA in complex with (S)-2-cyano-1-(2-m... -

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Entry
Database: PDB / ID: 3hpt
TitleCrystal structure of human FxA in complex with (S)-2-cyano-1-(2-methylbenzofuran-5-yl)-3-(2-oxo-1-(2-oxo-2-(pyrrolidin-1-yl)ethyl)azepan-3-yl)guanidine
Components(Coagulation factor ...Coagulation) x 2
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 / 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 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 / Chem-YET / Coagulation factor X
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsKlei, H.E. / Ghosh, K. / Rushith, A. / Kish, K.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2009
Title: Cyanoguanidine-based lactam derivatives as a novel class of orally bioavailable factor Xa inhibitors.
Authors: Shi, Y. / Zhang, J. / Shi, M. / O'Connor, S.P. / Bisaha, S.N. / Li, C. / Sitkoff, D. / Pudzianowski, A.T. / Chong, S. / Klei, H.E. / Kish, K. / Yanchunas, J. / Liu, E.C. / Hartl, K.S. / ...Authors: Shi, Y. / Zhang, J. / Shi, M. / O'Connor, S.P. / Bisaha, S.N. / Li, C. / Sitkoff, D. / Pudzianowski, A.T. / Chong, S. / 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
DepositionJun 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 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: Coagulation factor X
B: Coagulation factor X
C: Coagulation factor X
D: Coagulation factor X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,64927
Polymers74,1704
Non-polymers2,47923
Water9,980554
1
A: Coagulation factor X
B: Coagulation factor X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,37014
Polymers37,0852
Non-polymers1,28512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-8.1 kcal/mol
Surface area15780 Å2
MethodPISA
2
C: Coagulation factor X
D: Coagulation factor X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,27813
Polymers37,0852
Non-polymers1,19311
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-10.4 kcal/mol
Surface area15840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.980, 78.660, 73.670
Angle α, β, γ (deg.)90.00, 102.49, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE BIOLOGICAL UNIT CONSISTS OF ONE LIGHT CHAIN (EGF-LIKE DOMAIN) AND ONE HEAVY CHAIN (CATALYTIC DOMAIN). THE ASYMMETRIC UNIT CONTAINS TWO BIOLOGICAL UNITS (CHAINS A,B AND CHAINS C,D). CHAINS A AND C ARE EGF-LIKE DOMAINS. CHAINS B AND D ARE CATALYTIC DOMAINS.

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Components

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

#1: Protein Coagulation factor X / Factor X / Stuart factor / Stuart-Prower factor / Factor X light chain


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


Mass: 26871.623 Da / Num. of mol.: 2
Fragment: Activated factor Xa heavy chain: UNP residues 235-472
Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: Blood / References: UniProt: P00742, coagulation factor Xa

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Non-polymers , 8 types, 577 molecules

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


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-YET / 1-cyano-2-(2-methyl-1-benzofuran-5-yl)-3-[(3S)-2-oxo-1-(2-oxo-2-pyrrolidin-1-ylethyl)azepan-3-yl]guanidine


Mass: 436.507 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H28N6O3
#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.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#9: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 554 / 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: 2.36 Å3/Da / Density % sol: 47.97 %
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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 7, 1999 / Details: Osmic mirrors
RadiationMonochromator: Yale/MSC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. obs: 35677 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 14.8
Reflection shellResolution: 2.19→2.28 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 2.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.665 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.28 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23868 1781 5 %RANDOM
Rwork0.17567 ---
obs0.17886 33872 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.605 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å2-0.59 Å2
2---0.05 Å20 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 2.19→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4915 0 162 554 5631
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225236
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3261.9757070
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8315647
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.07824.267232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.07915842
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2781530
X-RAY DIFFRACTIONr_chiral_restr0.080.2750
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023974
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.22444
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.23533
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2561
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1210.210
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.271
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.238
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6621.53223
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.23625131
X-RAY DIFFRACTIONr_scbond_it1.54132093
X-RAY DIFFRACTIONr_scangle_it2.5444.51931
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.19→2.24 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 102 -
Rwork0.21 2393 -
obs--94.08 %

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