6EDB Transferase Dna date Aug 09, 2018
title Crystal Structure Of Sry.Hcgas-21bp Dsdna Complex
authors W.Xie, L.Lama, C.Adura, J.F.Glickman, T.Tuschl, D.J.Patel
compound source
Molecule: Sex-Determining Region Y Protein,Cyclic Gmp-Amp S
Chain: A, B
Synonym: Testis-Determining Factor,H-Cgas,2'3'-Cgamp Syntha Domain-Containing Protein 1;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Sry, Tdf, Cgas, C6orf150, Mb21d1
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

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

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

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

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
symmetry Space Group: I 2 2 2
R_factor 0.255 R_Free 0.302
length a length b length c angle alpha angle beta angle gamma
90.307 115.827 159.077 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.21 Å
ligand ZN enzyme Transferase E.C. BRENDA
Primary referenceHuman cGAS catalytic domain has an additional DNA-binding interface that enhances enzymatic activity and liquid-phase condensation., Xie W, Lama L, Adura C, Tomita D, Glickman JF, Tuschl T, Patel DJ, Proc Natl Acad Sci U S A. 2019 May 29. pii: 1905013116. doi:, 10.1073/pnas.1905013116. PMID:31142647
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (97 Kb) [Save to disk]
  • Biological Unit Coordinates (6edb.pdb1.gz) 90 Kb
  • LPC: Ligand-Protein Contacts for 6EDB
  • CSU: Contacts of Structural Units for 6EDB
  • Structure Factors (76 Kb)
  • Retrieve 6EDB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6EDB from S2C, [Save to disk]
  • View 6EDB 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 6EDB
  • 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 6edb from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6edb_A] [6edb_D] [6edb_C] [6edb_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6EDB
  • Community annotation for 6EDB at PDBWiki (http://pdbwiki.org)

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