4Y60 Transcription Dna date Feb 12, 2015
title Structure Of Sox18-Hmgprox1-Dna
authors K.Narasimhan, N.Prokoph, P.Kolatkar, H.Robinson, R.Jauch
compound source
Molecule: Transcription Factor Sox-18
Chain: C
Fragment: Unp Residues 77-155
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Sox18, Sox-18
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'- D(Cpapcptpapgpcpaptptpgptpcptpgpgpg)-3');
Chain: A
Engineered: Yes

Synthetic: Yes
Organism_scientific: Mus Musculus
Organism_taxid: 10090

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

Synthetic: Yes
Organism_scientific: Mus Musculus
Organism_taxid: 10090
symmetry Space Group: P 64
R_factor 0.174 R_Free 0.199
length a length b length c angle alpha angle beta angle gamma
111.942 111.942 32.417 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.75 Å
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (67 Kb) [Save to disk]
  • Biological Unit Coordinates (4y60.pdb1.gz) 60 Kb
  • CSU: Contacts of Structural Units for 4Y60
  • Structure Factors (350 Kb)
  • Retrieve 4Y60 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4Y60 from S2C, [Save to disk]
  • Re-refined 4y60 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4Y60 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 4Y60
  • 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
  • Fold representative 4y60 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4y60_C] [4y60_A] [4y60_B] [4y60]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4Y60: [HMG ] by SMART
  • Other resources with information on 4Y60
  • Community annotation for 4Y60 at PDBWiki (http://pdbwiki.org)

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