1WOG Hydrolase date Aug 18, 2004
title Crystal Structure Of Agmatinase Reveals Structural Conservat Inhibition Mechanism Of The Ureohydrolase Superfamily
authors H.J.Ahn, K.H.Kim, J.Lee, J.Y.Ha, H.H.Lee, D.Kim, H.J.Yoon, A.R.K S.W.Suh
compound source
Molecule: Agmatinase
Chain: A, B, C, D, E, F
Ec: 3.5.3.11
Engineered: Yes
 Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.223 R_Free 0.251
crystal
cell
length a length b length c angle alpha angle beta angle gamma
81.769 131.436 168.854 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand 16D, MN enzyme Hydrolase E.C.3.5.3.11 BRENDA
related structures by homologous chain: 1WOH, 1WOI
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, E, B


Primary referenceCrystal structure of agmatinase reveals structural conservation and inhibition mechanism of the ureohydrolase superfamily., Ahn HJ, Kim KH, Lee J, Ha JY, Lee HH, Kim D, Yoon HJ, Kwon AR, Suh SW, J Biol Chem 2004 Nov 26;279(48):50505-13. Epub . PMID:15355972
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (290 Kb) [Save to disk]
  • Biological Unit Coordinates (1wog.pdb1.gz) 284 Kb
  • LPC: Ligand-Protein Contacts for 1WOG
  • CSU: Contacts of Structural Units for 1WOG
  • Likely Quarternary Molecular Structure file(s) for 1WOG
  • Structure Factors (1421 Kb)
  • Retrieve 1WOG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1WOG from S2C, [Save to disk]
  • Re-refined 1wog structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1WOG 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 1WOG
  • 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 1WOG, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1woga_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1wogb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1wogc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1wogd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1woge_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1wogf_, region F [Jmol] [rasmolscript] [script source]
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1wog_C] [1wog] [1wog_F] [1wog_A] [1wog_E] [1wog_B] [1wog_D]
  • SWISS-PROT database: [Q9RZ04]
  • Domain organization of [Q9RZ04_DEIRA] by SWISSPFAM
    • Other resources with information on 1WOG
  • Community annotation for 1WOG 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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