1LJM Transcription date Apr 22, 2002
title Dna Recognition Is Mediated By Conformational Transition And By Dna Bending
authors D.Bartfeld, L.Shimon, G.C.Couture, D.Rabinovich, F.Frolow, D.Levanon, Y.Groner, Z.Shakked
compound source
Molecule: Runx1 Transcription Factor
Chain: A, B
Fragment: Runt Domain
Synonym: Runt-Related Transcription Factor 1, Acute Myeloid Leukemia 1 Protein, Core-Binding Factor, Alpha 2 Subunit;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Human
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Phs2
Expression_system_vector_type: Pv8+Lambdapl+Rbs
Expression_system_plasmid: Runt-Pv-8
symmetry Space Group: H 3 2
R_factor 0.193 R_Free 0.249
length a length b length c angle alpha angle beta angle gamma
121.230 121.230 186.330 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.50 Å
ligand CL enzyme
related structures by homologous chain: 1EAN, 1H9D
A, B

Primary referenceDNA recognition by the RUNX1 transcription factor is mediated by an allosteric transition in the RUNT domain and by DNA bending., Bartfeld D, Shimon L, Couture GC, Rabinovich D, Frolow F, Levanon D, Groner Y, Shakked Z, Structure (Camb) 2002 Oct;10(10):1395-407. PMID:12377125
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (45 Kb) [Save to disk]
  • Biological Unit Coordinates (1ljm.pdb1.gz) 22 Kb
  • Biological Unit Coordinates (1ljm.pdb2.gz) 21 Kb
  • Biological Unit Coordinates (1ljm.pdb3.gz) 80 Kb
  • Biological Unit Coordinates (1ljm.pdb4.gz) 40 Kb
  • LPC: Ligand-Protein Contacts for 1LJM
  • CSU: Contacts of Structural Units for 1LJM
  • Likely Quarternary Molecular Structure file(s) for 1LJM
  • Retrieve 1LJM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1LJM from S2C, [Save to disk]
  • View 1LJM 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 1LJM
  • 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 1LJM, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ljma_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1ljmb_, region B [Jmol] [rasmolscript] [script source]
  • Fold representative 1ljm from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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: [1ljm] [1ljm_A] [1ljm_B]
  • SWISS-PROT database: [Q01196]
  • Domain organization of [RUNX1_HUMAN] by SWISSPFAM
  • Other resources with information on 1LJM
  • Community annotation for 1LJM 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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