5D9I Replication Dna date Aug 18, 2015
title Sv40 Large T Antigen Origin Binding Domain Bound To Artifici Fork
authors G.Meinke, A.Bohm, P.A.Bullock
compound source
Molecule: Large T Antigen
Chain: A, B
Fragment: Unp Residues 131-260
Synonym: Lt-Ag
Ec: 3.6.4.-
Engineered: Yes
Organism_scientific: Simian Virus 40
Organism_common: Sv40
Organism_taxid: 10633
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_plasmid: Pgex-1lambdat

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

Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Expression_system: Synthetic Construct
Expression_system_taxid: 32630

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

Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Expression_system: Synthetic Construct
Expression_system_taxid: 32630
symmetry Space Group: C 1 2 1
R_factor 0.180 R_Free 0.223
crystal
cell
length a length b length c angle alpha angle beta angle gamma
94.192 63.393 64.891 90.00 92.42 90.00
method X-Ray Diffractionresolution 1.70 Å
ligand ACT, CA, CME, EDO enzyme Hydrolase E.C.3.6.4 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructure-based analysis of the interaction between the simian virus 40 T-antigen origin binding domain and single-stranded DNA., Meinke G, Phelan PJ, Fradet-Turcotte A, Bohm A, Archambault J, Bullock PA, J Virol. 2011 Jan;85(2):818-27. Epub 2010 Oct 27. PMID:20980496
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (140 Kb) [Save to disk]
  • Biological Unit Coordinates (5d9i.pdb1.gz) 134 Kb
  • LPC: Ligand-Protein Contacts for 5D9I
  • CSU: Contacts of Structural Units for 5D9I
  • Structure Factors (991 Kb)
  • Retrieve 5D9I in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5D9I from S2C, [Save to disk]
  • Re-refined 5d9i structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5D9I 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 5D9I
  • 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 5d9i from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5d9i_B] [5d9i_X] [5d9i_A] [5d9i_Y] [5d9i]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5D9I
  • Community annotation for 5D9I at PDBWiki (http://pdbwiki.org)

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