2OD8	Protein Binding	date	Dec 21, 2006
title	Structure Of A Peptide Derived From Cdc9 Bound To Pcna
authors	B.R.Chapados, J.A.Tainer
compound		source
Molecule: Proliferating Cell Nuclear Antigen Chain: A Synonym: Pcna Engineered: Yes		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932 Gene: Pol30 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pt7-Pcna
Molecule: Dna Ligase I, Mitochondrial Precursor Chain: B Fragment: Residues 32-53 Synonym: Cdc9, Polydeoxyribonucleotide Synthase Ec: 6.5.1.1 Engineered: Yes		Synthetic: Yes Other_details: Peptide Synthesized Based On Cdc9 Sequence ( P04819), Residues 32-53.
symmetry	Space Group: I 2 3	R_factor 0.247 R_Free 0.285
crystal cell	length a length b length c angle alpha angle beta angle gamma 139.280 139.280 139.280 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.80 Å
ligand		enzyme	Ligase E.C.6.5.1.1 BRENDA
Gene Ontology	Chain Function Process Component A chromatin silencing at telom...
Primary reference	The C-terminal domain of yeast PCNA is required for physical and functional interactions with Cdc9 DNA ligase., Vijayakumar S, Chapados BR, Schmidt KH, Kolodner RD, Tainer JA, Tomkinson AE, Nucleic Acids Res. 2007;35(5):1624-37. Epub 2007 Feb 18. PMID:17308348

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (47 Kb) [Save to disk] Biological Unit Coordinates (2od8.pdb1.gz) 122 Kb CSU: Contacts of Structural Units for 2OD8 Likely Quarternary Molecular Structure file(s) for 2OD8 Structure Factors (156 Kb) Retrieve 2OD8 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2OD8 from S2C, [Save to disk] Re-refined 2od8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2OD8 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 2OD8

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 2OD8, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2od8] [2od8_B] [2od8_A] SWISS-PROT database: [P04819] [P15873] Domain organization of [DNLI1_YEAST] [PCNA_YEAST] by SWISSPFAM

Other resources with information on 2OD8

Community annotation for 2OD8 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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