2LD5 Transcription Dna date May 14, 2011
title Solution Nmr-Derived Complex Structure Of Hoxa13 Dna Binding Bound To Dna
authors Y.Zhang
compound source
Molecule: Homeobox Protein Hox-A13
Chain: A
Fragment: Homeobox Dna Binding Residues 320-386
Synonym: Homeobox Protein Hox-1.10
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Hox-1.10, Hoxa13
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector: Pet-15b

Molecule: Dna (5'-D(Cpapapaptpapapapaptpc)-3')
Chain: B
Engineered: Yes

Synthetic: Yes

Molecule: Dna (5'-D(Pgpaptptptptpaptptptpg)-3')
Chain: C
Engineered: Yes

Synthetic: Yes
methodSolution NMR
note 2LD5 is a representative structure

Primary referenceStructural basis for sequence specific DNA binding and protein dimerization of HOXA13., Zhang Y, Larsen CA, Stadler HS, Ames JB, PLoS One. 2011;6(8):e23069. Epub 2011 Aug 1. PMID:21829694
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (246 Kb) [Save to disk]
  • Biological Unit Coordinates (2ld5.pdb1.gz) 25 Kb
  • CSU: Contacts of Structural Units for 2LD5
  • Original NMR restraints for 2LD5 from PDB
  • Retrieve 2LD5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2LD5 from S2C, [Save to disk]
  • View 2LD5 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 2LD5
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2LD5, from MSDmotif at EBI
  • Fold representative 2ld5 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ld5_A] [2ld5_C] [2ld5] [2ld5_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 2LD5: [HOX ] by SMART
  • Other resources with information on 2LD5
  • Community annotation for 2LD5 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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