1KMK Lyase date Dec 16, 2001
title E. Coli Nifscsdb Protein At 2.20a With The Cysteine Persele Intermediate (Residue Csz).
authors C.D.Lima, S.K.Burley, New York Sgx Research Center For Structu Genomics (Nysgxrc)
compound source
Molecule: Selenocysteine Lyase
Chain: A
Synonym: Nifscsdb, Selenocysteine Reductase, Selenocystein Lyase, Scl;
Ec: 4.4.1.16
Engineered: Yes
 Organism_scientific: Escherichia Coli
Organism_taxid: 562
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 43 21 2
R_factor 0.196 R_Free 0.239
crystal
cell
length a length b length c angle alpha angle beta angle gamma
125.855 125.855 133.200 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand CSZ, PLP, SEC enzyme Lyase E.C.4.4.1.16 BRENDA
related structures by homologous chain: 1C0N, 1JF9
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceAnalysis of the E. coli NifS CsdB protein at 2.0 A reveals the structural basis for perselenide and persulfide intermediate formation., Lima CD, J Mol Biol. 2002 Feb 1;315(5):1199-208. PMID:11827487
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (78 Kb) [Save to disk]
  • Biological Unit Coordinates (1kmk.pdb1.gz) 143 Kb
  • LPC: Ligand-Protein Contacts for 1KMK
  • CSU: Contacts of Structural Units for 1KMK
  • Likely Quarternary Molecular Structure file(s) for 1KMK
  • Structure Factors (729 Kb)
  • Retrieve 1KMK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1KMK from S2C, [Save to disk]
  • Re-refined 1kmk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1KMK 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 1KMK
  • 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 1KMK, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1kmka_, region A [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: [1kmk] [1kmk_A]
  • SWISS-PROT database: [P77444]
  • Domain organization of [SUFS_ECOLI] by SWISSPFAM
    • Other resources with information on 1KMK
  • Community annotation for 1KMK 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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