3K9X Hydrolase date Oct 16, 2009
title X-Ray Crystal Structure Of Human Fxa In Complex With (S)-N-( Methylbenzofuran-5-Ylamino)(2-Oxo-1-(2-Oxo-2- (Pyrrolidin-1 Ethyl)Azepan-3- Ylamino)Methylene)Nicotinamide
authors H.E.Klei, K.Kish, K.Ghosh, A.Rushith
compound source
Molecule: Protein (Coagulation Factor X)
Chain: A, C
Fragment: Egf-Like Domains (Unp Residues 85 To 178)
Synonym: Stuart Factor, Stuart-Prower Factor, Factor X Ligh Factor X Heavy Chain, Activated Factor Xa Heavy Chain;
Ec: 3.4.21.6
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Secretion: Blood

Molecule: Protein (Coagulation Factor X)
Chain: B, D
Fragment: Catalytic Domains (Unp Residues 235 To 472)
Synonym: Stuart Factor, Stuart-Prower Factor, Factor X Ligh Factor X Heavy Chain, Activated Factor Xa Heavy Chain;
Ec: 3.4.21.6

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Secretion: Blood
symmetry Space Group: P 1 21 1
R_factor 0.176 R_Free 0.240
crystal
cell
length a length b length c angle alpha angle beta angle gamma
62.263 77.630 73.732 90.00 102.63 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand CA, GOL, MBM, NA BindingDB enzyme Hydrolase E.C.3.4.21.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C


D, B


Primary referenceAroylguanidine-based factor Xa inhibitors: the discovery of BMS-344577., Shi Y, Li C, O'Connor SP, Zhang J, Shi M, Bisaha SN, Wang Y, Sitkoff D, Pudzianowski AT, Huang C, Klei HE, Kish K, Yanchunas J Jr, Liu EC, Hartl KS, Seiler SM, Steinbacher TE, Schumacher WA, Atwal KS, Stein PD, Bioorg Med Chem Lett. 2009 Dec 15;19(24):6882-9. Epub 2009 Oct 23. PMID:19896847
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (125 Kb) [Save to disk]
  • Biological Unit Coordinates (3k9x.pdb1.gz) 62 Kb
  • Biological Unit Coordinates (3k9x.pdb2.gz) 60 Kb
  • LPC: Ligand-Protein Contacts for 3K9X
  • CSU: Contacts of Structural Units for 3K9X
  • Structure Factors (364 Kb)
  • Retrieve 3K9X in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3K9X from S2C, [Save to disk]
  • Re-refined 3k9x structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3K9X in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3K9X
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3K9X, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3k9x] [3k9x_C] [3k9x_A] [3k9x_D] [3k9x_B]
  • SWISS-PROT database: [P00742]
  • Domain organization of [FA10_HUMAN] by SWISSPFAM
  • Domains found in 3K9X: [EGF_CA] [EGF_like] [Tryp_SPc ] by SMART
  • Other resources with information on 3K9X
  • Community annotation for 3K9X at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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