4EUW Transcription Dna date Apr 25, 2012
title Crystal Structure Of A Hmg Domain Of Transcription Factor So To Dna (Sox-9dna) From Homo Sapiens At 2.77 A Resolution
authors Joint Center For Structural Genomics (Jcsg), Partnership For Biology (Stemcell)
compound source
Molecule: Transcription Factor Sox-9
Chain: A
Fragment: Hmg Box Containing Residues 98-181
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Sgt82680, Sox9
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)Phager20080807
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Prsf2ek6tevlic

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

Synthetic: Yes
Other_details: Sequence Matching The Sox-9 Binding Site Fro Anti-Mullerian Hormone (Amh) Promoter, Top Strand;

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

Synthetic: Yes
Other_details: Sequence Matching The Sox-9 Binding Site Fro Anti-Mullerian Hormone (Amh) Promoter, Bottom Strand
symmetry Space Group: C 2 2 2
R_factor 0.247 R_Free 0.278
length a length b length c angle alpha angle beta angle gamma
55.772 134.654 49.987 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.77 Å
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (51 Kb) [Save to disk]
  • Biological Unit Coordinates (4euw.pdb1.gz) 46 Kb
  • CSU: Contacts of Structural Units for 4EUW
  • Structure Factors (246 Kb)
  • Retrieve 4EUW in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4EUW from S2C, [Save to disk]
  • Re-refined 4euw structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4EUW 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 4EUW
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4EUW, from MSDmotif at EBI
  • Fold representative 4euw from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4euw_A] [4euw] [4euw_B] [4euw_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4EUW: [HMG ] by SMART
  • Alignments of the sequence of 4EUW with the sequences similar proteins can be viewed for 4EUW's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • Other resources with information on 4EUW
  • Community annotation for 4EUW at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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