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- PDB-1kig: BOVINE FACTOR XA -

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Basic information

Entry
Database: PDB / ID: 1kig
TitleBOVINE FACTOR XA
Components
  • (FACTOR XA) x 2
  • ANTICOAGULANT PEPTIDE
KeywordsCOMPLEX (PROTEASE/INHIBITOR) / GLYCOPROTEIN / SERINE PROTEASE / PLASMA / BLOOD COAGULATION / COMPLEX (PROTEASE-INHIBITOR) / COMPLEX (PROTEASE-INHIBITOR) complex
Function / homology
Function and homology information


coagulation factor Xa / serine-type endopeptidase inhibitor activity / blood coagulation / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space
Similarity search - Function
Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla domain superfamily / Pancreatic trypsin inhibitor Kunitz domain superfamily / Laminin / Laminin / Coagulation Factor Xa inhibitory site / EGF-like domain ...Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla domain superfamily / Pancreatic trypsin inhibitor Kunitz domain superfamily / Laminin / Laminin / Coagulation Factor Xa inhibitory site / 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 1. / EGF-like domain signature 2. / EGF-like domain / Ribbon / Few Secondary Structures / Irregular / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / 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
Coagulation factor X / Tick anticoagulant peptide
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Ornithodoros moubata (arthropod)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsWei, A. / Alexander, R. / Chang, C.-H.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: Unexpected binding mode of tick anticoagulant peptide complexed to bovine factor Xa.
Authors: Wei, A. / Alexander, R.S. / Duke, J. / Ross, H. / Rosenfeld, S.A. / Chang, C.H.
History
DepositionApr 24, 1997Processing site: BNL
Revision 1.0Oct 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: FACTOR XA
L: FACTOR XA
I: ANTICOAGULANT PEPTIDE


Theoretical massNumber of molelcules
Total (without water)39,4733
Polymers39,4733
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.100, 133.100, 68.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein FACTOR XA


Mass: 26847.541 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Organ: BLOOD / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00743, coagulation factor Xa
#2: Protein FACTOR XA


Mass: 5633.237 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Organ: BLOOD / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00743, coagulation factor Xa
#3: Protein ANTICOAGULANT PEPTIDE / RTAP


Mass: 6992.614 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ornithodoros moubata (arthropod) / Organ: BLOOD / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P17726
Compound detailsTHE TWO CHAINS OF BOVINE FACTOR XA ARE FORMED FROM A SINGLE-CHAIN PRECURSOR BY THE EXCISION OF TWO ...THE TWO CHAINS OF BOVINE FACTOR XA ARE FORMED FROM A SINGLE-CHAIN PRECURSOR BY THE EXCISION OF TWO ARG RESIDUES AND ARE HELD TOGETHER BY ONE OR MORE DISULFIDE BONDS.
Has protein modificationY
Sequence detailsTHE RESIDUE NUMBERING SCHEME WAS CHOSEN TO PROVIDE MAXIMUM HOMOLOGY WITH THE SEQUENCE OF CHYMOTRYPSIN.
Source detailsTHE RTAP INHIBITOR WAS PRODUCED BY RECOMBINANT DNA METHODOLOGIES AND EXPRESSED IN YEAST.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.86 Å3/Da / Density % sol: 68.12 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMsodium potassium phosphate1reservoir
20.1 M1reservoirNaCl
312 %PEG80001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 3 Å / Num. obs: 10255 / % possible obs: 83 % / Num. measured all: 67914 / Rmerge(I) obs: 0.114

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.187 / Rfactor obs: 0.187 / Highest resolution: 3 Å
Refinement stepCycle: LAST / Highest resolution: 3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2756 0 0 0 2756
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Num. reflection obs: 9573 / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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