2FCC Hydrolase date Dec 12, 2005
title Crystal Structure Of T4 Pyrimidine Dimer Glycosylase (T4-Pdg Covalently Complexed With A Dna Substrate Containing Abasic
authors G.Golan, D.O.Zharkov, A.S.Fernandes, M.L.Dodson, A.K.Mccullough, A.P.Grollman, R.S.Lloyd, G.Shoham
compound source
Molecule: Dna (5'-D(Cpcpapgpgpap(Ped)Pgpapapgpc
Chain: C, E
Fragment: Ds Oligonucleotide Containing Ap Site
Engineered: Yes
Synthetic: Yes
Other_details: Chemically Synthesized.

Molecule: Dna (5'-D(Gpgpcp(Bru)P(Bru)Pcpap(Bru)Pcp Pgpg)-3');
Chain: D, F
Engineered: Yes

Synthetic: Yes
Other_details: Chemically Synthesized.

Molecule: Endonuclease V
Chain: A, B
Fragment: T4-Pdg
Ec: 3.1.25.1
Engineered: Yes

Organism_scientific: Enterobacteria Phage T4
Organism_taxid: 10665
Gene: Denv
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Ab2480
symmetry Space Group: P 64 2 2
R_factor 0.249 R_Free 0.274
crystal
cell
length a length b length c angle alpha angle beta angle gamma
184.059 184.059 100.855 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.30 Å
ligand BRU, GOL, PED, SO4 enzyme Hydrolase E.C.3.1.25.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • nuclease activity
  • endonuclease activity


  • Primary referenceStructure of T4 Pyrimidine Dimer Glycosylase in a Reduced Imine Covalent Complex with Abasic Site-containing DNA., Golan G, Zharkov DO, Grollman AP, Dodson ML, McCullough AK, Lloyd RS, Shoham G, J Mol Biol. 2006 Sep 15;362(2):241-58. Epub 2006 Jul 7. PMID:16916523
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (78 Kb) [Save to disk]
  • Biological Unit Coordinates (2fcc.pdb1.gz) 38 Kb
  • Biological Unit Coordinates (2fcc.pdb2.gz) 36 Kb
  • LPC: Ligand-Protein Contacts for 2FCC
  • CSU: Contacts of Structural Units for 2FCC
  • Likely Quarternary Molecular Structure file(s) for 2FCC
  • Structure Factors (1201 Kb)
  • Retrieve 2FCC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2FCC from S2C, [Save to disk]
  • Re-refined 2fcc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2FCC 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 2FCC
  • 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 2FCC, from MSDmotif at EBI
  • Fold representative 2fcc from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2fcc_D] [2fcc] [2fcc_F] [2fcc_E] [2fcc_B] [2fcc_A] [2fcc_C]
  • SWISS-PROT database: [P04418]
  • Domain organization of [END5_BPT4] by SWISSPFAM
  • Other resources with information on 2FCC
  • Community annotation for 2FCC at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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