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- PDB-2h9e: Crystal Structure of FXa/selectide/NAPC2 ternary complex -

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Basic information

Entry
Database: PDB / ID: 2h9e
TitleCrystal Structure of FXa/selectide/NAPC2 ternary complex
Components
  • (Coagulation factor X ...) x 2
  • Anti-coagulant protein C2
  • selectide inhibitor DTY-ILE-ARG-LEU-LPD peptide
KeywordsHYDROLASE/HYDROLASE INHIBITOR / factor Xa / NAPc2 / selectide / hydrolase-hydrolase inhibitor complex / blood clotting
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 / serine-type endopeptidase inhibitor activity / 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
Trypsin Inhibitor-like, cysteine rich domain / Serine protease inhibitor-like superfamily / Trypsin Inhibitor like cysteine rich domain / 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 ...Trypsin Inhibitor-like, cysteine rich domain / Serine protease inhibitor-like superfamily / Trypsin Inhibitor like cysteine rich domain / 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
ACETATE ION / PHOSPHATE ION / Coagulation factor X / Anti-coagulant protein C2
Similarity search - Component
Biological speciesAncylostoma caninum (dog hookworm)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMurakami, M.T. / Geiger, G. / Tulinsky, A. / Arni, R.K.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Intermolecular Interactions and Characterization of the Novel Factor Xa Exosite Involved in Macromolecular Recognition and Inhibition: Crystal Structure of Human Gla-domainless Factor Xa ...Title: Intermolecular Interactions and Characterization of the Novel Factor Xa Exosite Involved in Macromolecular Recognition and Inhibition: Crystal Structure of Human Gla-domainless Factor Xa Complexed with the Anticoagulant Protein NAPc2 from the Hematophagous Nematode Ancylostoma caninum.
Authors: Murakami, M.T. / Rios-Steiner, J. / Weaver, S.E. / Tulinsky, A. / Geiger, J.H. / Arni, R.K.
History
DepositionJun 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Coagulation factor X heavy chain
L: Coagulation factor X light chain
C: Anti-coagulant protein C2
S: selectide inhibitor DTY-ILE-ARG-LEU-LPD peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,80414
Polymers53,0344
Non-polymers77010
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6490 Å2
ΔGint-60 kcal/mol
Surface area15610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.945, 86.410, 145.892
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is the chain H (catalytic domain or heavy chain) and chain L (EGF2 domain or light chain), which forms the Gla-domainless factor Xa

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Components

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Coagulation factor X ... , 2 types, 2 molecules HL

#1: Protein Coagulation factor X heavy chain


Mass: 26346.000 Da / Num. of mol.: 1 / Fragment: catalytic domain / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00742, coagulation factor Xa
#2: Protein Coagulation factor X light chain


Mass: 16366.871 Da / Num. of mol.: 1 / Fragment: EGF-like 1 domain / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00742, coagulation factor Xa

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Protein / Protein/peptide , 2 types, 2 molecules CS

#3: Protein Anti-coagulant protein C2


Mass: 9660.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ancylostoma caninum (dog hookworm) / Production host: Escherichia coli (E. coli) / References: UniProt: Q16938
#4: Protein/peptide selectide inhibitor DTY-ILE-ARG-LEU-LPD peptide


Mass: 660.829 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED.

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Non-polymers , 4 types, 268 molecules

#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: peg 8000, potassium dihydrogen phosphate, acetate ion, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1.01 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 9, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.01 Å / Relative weight: 1
ReflectionResolution: 2.2→37.17 Å / Num. all: 32280 / Num. obs: 32172 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2
Reflection shellResolution: 2.2→2.26 Å / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→74.33 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.915 / SU B: 4.984 / SU ML: 0.131 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.195 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26832 1631 5.1 %RANDOM
Rwork0.21959 ---
all0.233 32172 --
obs0.22209 30145 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.472 Å2
Baniso -1Baniso -2Baniso -3
1--4.36 Å20 Å20 Å2
2---0.95 Å20 Å2
3---5.31 Å2
Refinement stepCycle: LAST / Resolution: 2.2→74.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2637 0 43 258 2938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0222736
X-RAY DIFFRACTIONr_angle_refined_deg2.1421.9613693
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.695332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.97624.436133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.02915458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9331517
X-RAY DIFFRACTIONr_chiral_restr0.2160.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022078
X-RAY DIFFRACTIONr_nbd_refined0.2440.21280
X-RAY DIFFRACTIONr_nbtor_refined0.3190.21768
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2540.2253
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2660.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2430.25
X-RAY DIFFRACTIONr_mcbond_it1.3391.51676
X-RAY DIFFRACTIONr_mcangle_it2.35422676
X-RAY DIFFRACTIONr_scbond_it3.40331094
X-RAY DIFFRACTIONr_scangle_it4.954.51017
LS refinement shellResolution: 2.2→2.255 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 127 -
Rwork0.241 2186 -
obs--98.47 %

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