4GDF Hydrolase Dna date Jul 31, 2012
title A Crystal Structure Of Sv40 Large T Antigen
authors Y.P.Chang, M.Xu, X.S.Chen
compound source
Molecule: Large T Antigen
Chain: A, B, E, F
Fragment: Unp Residues 131-627
Engineered: Yes
Organism_scientific: Simian Virus 40
Organism_common: Sv40
Organism_taxid: 10633
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (32-Mer)
Chain: C, G
Engineered: Yes

Synthetic: Yes
Other_details: Nucleic Acid Synthesis

Molecule: Dna (32-Mer)
Chain: D, H
Engineered: Yes

Synthetic: Yes
Other_details: Nucleic Acid Synthesis
symmetry Space Group: P 1 21 1
R_factor 0.227 R_Free 0.255
length a length b length c angle alpha angle beta angle gamma
73.633 128.307 166.120 90.00 89.91 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand ZN enzyme
F, A, E, B

Primary referenceMechanism of Origin DNA Recognition and Assembly of an Initiator-Helicase Complex by SV40 Large Tumor Antigen., Chang YP, Xu M, Machado AC, Yu XJ, Rohs R, Chen XS, Cell Rep. 2013 Mar 27. pii: S2211-1247(13)00109-5. doi:, 10.1016/j.celrep.2013.03.002. PMID:23545501
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (384 Kb) [Save to disk]
  • Biological Unit Coordinates (4gdf.pdb1.gz) 191 Kb
  • Biological Unit Coordinates (4gdf.pdb2.gz) 192 Kb
  • LPC: Ligand-Protein Contacts for 4GDF
  • CSU: Contacts of Structural Units for 4GDF
  • Structure Factors (794 Kb)
  • Retrieve 4GDF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4GDF from S2C, [Save to disk]
  • Re-refined 4gdf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4GDF 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 4GDF
  • 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 4GDF, from MSDmotif at EBI
  • Fold representative 4gdf from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4gdf_F] [4gdf_D] [4gdf_B] [4gdf_H] [4gdf] [4gdf_C] [4gdf_G] [4gdf_A] [4gdf_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4GDF
  • Community annotation for 4GDF at PDBWiki (http://pdbwiki.org)

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