2D1S Oxidoreductase date Aug 31, 2005
title Crystal Structure Of The Thermostable Japanese Firefly Lucif Complexed With High-Energy Intermediate Analogue
authors T.Nakatsu, S.Ichiyama, J.Hiratake, A.Saldanha, N.Kobashi, K.Sakat Riken Structural Genomicsproteomics Initiative (Rsgi)
compound source
Molecule: Luciferin 4-Monooxygenase
Chain: A
Synonym: Luciferase
Ec: 1.13.12.7
Engineered: Yes
Mutation: Yes
Organism_scientific: Luciola Cruciata
Organism_common: Japanese Firefly
Organism_taxid: 7051
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Hb101
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Puc18
symmetry Space Group: P 21 21 21
R_factor 0.180 R_Free 0.201
crystal
cell
length a length b length c angle alpha angle beta angle gamma
57.586 181.313 52.038 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.30 Å
ligand CL, CSO, SLU enzyme Oxidoreductase E.C.1.13.12.7 BRENDA
note 2D1S (Molecule of the Month:pdb78)is a representative structure
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural basis for the spectral difference in luciferase bioluminescence., Nakatsu T, Ichiyama S, Hiratake J, Saldanha A, Kobashi N, Sakata K, Kato H, Nature. 2006 Mar 16;440(7082):372-6. PMID:16541080
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (101 Kb) [Save to disk]
  • Biological Unit Coordinates (2d1s.pdb1.gz) 97 Kb
  • LPC: Ligand-Protein Contacts for 2D1S
  • CSU: Contacts of Structural Units for 2D1S
  • Likely Quarternary Molecular Structure file(s) for 2D1S
  • Structure Factors (1020 Kb)
  • Retrieve 2D1S in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2D1S from S2C, [Save to disk]
  • Re-refined 2d1s structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2D1S 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 2D1S
  • 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 2D1S, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2d1s] [2d1s_A]
  • SWISS-PROT database: [P13129]
  • Domain organization of [LUCI_LUCCR] by SWISSPFAM
  • Other resources with information on 2D1S
  • Community annotation for 2D1S 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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