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 Diffraction	resolution	2.30 Å
ligand	BRU, GOL, PED, SO4	enzyme	Hydrolase E.C.3.1.25.1 BRENDA
Gene Ontology	Chain Function Process Component A, B nuclease activity endonuclease activity
Primary reference	Structure 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] (77 Kb) [Save to disk] Biological Unit Coordinates (2fcc.pdb1.gz) 37 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

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 3D motif for 2FCC, from MSDmotif at EBI

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)

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