1LK7 Isomerase date Apr 24, 2002
title Structure Of D-Ribose-5-Phosphate Isomerase From In Complex Phospho-Erythronic Acid
authors K.Ishikawa, I.Matsui, F.Payan, C.Cambillau, H.Ishida, Y.Kawarabay H.Kikuchi, A.Roussel
compound source
Molecule: D-Ribose-5-Phosphate Isomerase
Chain: A, B, C, D
Engineered: Yes
Organism_scientific: Pyrococcus Horikoshii
Organism_taxid: 53953
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet11a
symmetry Space Group: P 21 21 21
R_factor 0.202 R_Free 0.247
length a length b length c angle alpha angle beta angle gamma
73.689 114.923 119.578 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand CL, DER, NA enzyme Isomerase E.C. BRENDA
related structures by homologous chain: 1LK5
A, D, C, B

Primary referenceA hyperthermostable D-ribose-5-phosphate isomerase from Pyrococcus horikoshii characterization and three-dimensional structure., Ishikawa K, Matsui I, Payan F, Cambillau C, Ishida H, Kawarabayasi Y, Kikuchi H, Roussel A, Structure (Camb) 2002 Jun;10(6):877-86. PMID:12057201
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (155 Kb) [Save to disk]
  • Biological Unit Coordinates (1lk7.pdb1.gz) 149 Kb
  • LPC: Ligand-Protein Contacts for 1LK7
  • CSU: Contacts of Structural Units for 1LK7
  • Likely Quarternary Molecular Structure file(s) for 1LK7
  • Structure Factors (495 Kb)
  • Retrieve 1LK7 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1LK7 from S2C, [Save to disk]
  • Re-refined 1lk7 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1LK7 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 1LK7
  • 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 1LK7, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1lk7a1, region A:1-130,A:211-229 [Jmol] [rasmolscript] [script source]
        - Domain d1lk7a2, region A:131-210 [Jmol] [rasmolscript] [script source]
        - Domain d1lk7b1, region B:1-130,B:211-229 [Jmol] [rasmolscript] [script source]
        - Domain d1lk7b2, region B:131-210 [Jmol] [rasmolscript] [script source]
        - Domain d1lk7c1, region C:1-130,C:211-229 [Jmol] [rasmolscript] [script source]
        - Domain d1lk7c2, region C:131-210 [Jmol] [rasmolscript] [script source]
        - Domain d1lk7d1, region D:1-130,D:211-229 [Jmol] [rasmolscript] [script source]
        - Domain d1lk7d2, region D:131-210 [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1lk7_B] [1lk7_D] [1lk7_A] [1lk7_C] [1lk7]
  • SWISS-PROT database: [O50083]
  • Domain organization of [RPIA_PYRHO] by SWISSPFAM
  • Other resources with information on 1LK7
  • Community annotation for 1LK7 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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