5FD3 Transcription Dna date Dec 15, 2015
title Structure Of Lin54 Tesmin Domain Bound To Dna
authors A.H.Marceau, J.G.Felthousen, P.D.Goetsch, H.Lee, S.M.Tripathi, S. L.Litovchick, S.M.Rubin
compound source
Molecule: Protein Lin-54 Homolog
Chain: A, B
Fragment: Tesmin Domain (Unp Residues 515-646)
Synonym: Cxc Domain-Containing Protein 1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Lin54, Cxcdc1, Kiaa2037
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgev

Molecule: Dna (5'-D(Gpapgptptptpgpapapapcpt)-3'
Chain: C, H
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Dna (5'-D(Cpapgptptptpcpapapapcptpc)
Chain: D, I
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 1
R_factor 0.181 R_Free 0.238
length a length b length c angle alpha angle beta angle gamma
39.320 53.880 67.120 98.40 102.53 106.57
method X-Ray Diffractionresolution 2.42 Å
ligand ZN enzyme
Primary referenceStructural basis for LIN54 recognition of CHR elements in cell cycle-regulated promoters., Marceau AH, Felthousen JG, Goetsch PD, Iness AN, Lee HW, Tripathi SM, Strome S, Litovchick L, Rubin SM, Nat Commun. 2016 Jul 28;7:12301. doi: 10.1038/ncomms12301. PMID:27465258
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (121 Kb) [Save to disk]
  • Biological Unit Coordinates (5fd3.pdb1.gz) 57 Kb
  • Biological Unit Coordinates (5fd3.pdb2.gz) 57 Kb
  • LPC: Ligand-Protein Contacts for 5FD3
  • CSU: Contacts of Structural Units for 5FD3
  • Structure Factors (1259 Kb)
  • Retrieve 5FD3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5FD3 from S2C, [Save to disk]
  • Re-refined 5fd3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5FD3 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 5FD3
  • 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
  • Fold representative 5fd3 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5fd3_H] [5fd3_D] [5fd3_B] [5fd3_I] [5fd3_C] [5fd3_A] [5fd3]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5FD3: [CXC ] by SMART
  • Other resources with information on 5FD3
  • Community annotation for 5FD3 at PDBWiki (http://pdbwiki.org)

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