2PKP Lyase date Apr 18, 2007
title Crystal Structure Of 3-Isopropylmalate Dehydratase (Leud)Fro Methhanocaldococcus Jannaschii Dsm2661 (Mj1271)
authors J.Jeyakanthan, D.R.Gayathri, D.Velmurugan, Y.Agari, A.Ebihara, S.Kuramitsu, A.Shinkai, Y.Shiro, S.Yokoyama, Riken Structural Genomicsproteomics Initiative (Rsgi)
compound source
Molecule: Homoaconitase Small Subunit
Chain: A
Synonym: Isopropylmalate Isomerase 1, Alpha-Ipm Isomerase 1
Ec: 4.2.1.114
Engineered: Yes
Organism_scientific: Methanocaldococcus Jannaschii
Organism_taxid: 243232
Strain: Dsm 2661
Gene: Akse
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl-21 Condon Plus (De3)-Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet21a
symmetry Space Group: C 2 2 21
R_factor 0.201 R_Free 0.248
crystal
cell
length a length b length c angle alpha angle beta angle gamma
90.992 108.283 45.449 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand PEG, ZN enzyme Lyase E.C.4.2.1.114 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceSubstrate specificity determinants of the methanogen homoaconitase enzyme: structure and function of the small subunit., Jeyakanthan J, Drevland RM, Gayathri DR, Velmurugan D, Shinkai A, Kuramitsu S, Yokoyama S, Graham DE, Biochemistry. 2010 Mar 30;49(12):2687-96. PMID:20170198
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (34 Kb) [Save to disk]
  • Biological Unit Coordinates (2pkp.pdb1.gz) 57 Kb
  • Biological Unit Coordinates (2pkp.pdb2.gz) 29 Kb
  • LPC: Ligand-Protein Contacts for 2PKP
  • CSU: Contacts of Structural Units for 2PKP
  • Likely Quarternary Molecular Structure file(s) for 2PKP
  • Structure Factors (165 Kb)
  • Retrieve 2PKP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2PKP from S2C, [Save to disk]
  • Re-refined 2pkp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2PKP 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 2PKP
  • 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 2PKP, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2pkp] [2pkp_A]
  • SWISS-PROT database: [Q58667]
  • Domain organization of [HACB_METJA] by SWISSPFAM
  • Other resources with information on 2PKP
  • Community annotation for 2PKP 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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