2Q2U	Ligase Dna	date	May 29, 2007
title	Structure Of Chlorella Virus Dna Ligase-Product Dna Complex
authors	C.D.Lima, J.Nandakumar, P.A.Nair, P.Smith, S.Shuman
compound		source
Molecule: 5'-D(Tptpcpcpgpaptpapgptpgpgpgpgpt Apapt)-3'; Chain: E, G, I, K Engineered: Yes		Synthetic: Yes Other_details: Chemically Synthsized.
Molecule: 5'-D(Aptptpgpcpgpapcp(Omc) Pcpcpapcptpaptpcpgpgpapa)-3'; Chain: F, H, J, L Engineered: Yes		Synthetic: Yes Other_details: Chemically Synthsized.
Molecule: Chlorella Virus Dna Ligase Chain: A, B, C, D Engineered: Yes		Organism_scientific: Paramecium Bursaria Chlorella Virus 1 Organism_taxid: 10506 Strain: Chlorella Virus Gene: A544r Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet16b
symmetry	Space Group: P 1	R_factor 0.249 R_Free 0.283
crystal cell	length a length b length c angle alpha angle beta angle gamma 66.475 92.895 89.633 70.32 78.45 89.87
method	X-Ray Diffraction	resolution	3.00 Å
ligand	OMC	enzyme
Gene Ontology	Chain Function Process Component A, D, C, B
Primary reference	Structural basis for nick recognition by a minimal pluripotent DNA ligase., Nair PA, Nandakumar J, Smith P, Odell M, Lima CD, Shuman S, Nat Struct Mol Biol. 2007 Aug;14(8):770-8. Epub 2007 Jul 8. PMID:17618295

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (258 Kb) [Save to disk] Biological Unit Coordinates (2q2u.pdb1.gz) 65 Kb Biological Unit Coordinates (2q2u.pdb2.gz) 66 Kb Biological Unit Coordinates (2q2u.pdb3.gz) 65 Kb Biological Unit Coordinates (2q2u.pdb4.gz) 65 Kb LPC: Ligand-Protein Contacts for 2Q2U CSU: Contacts of Structural Units for 2Q2U Likely Quarternary Molecular Structure file(s) for 2Q2U Structure Factors (329 Kb) Retrieve 2Q2U in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2Q2U from S2C, [Save to disk] Re-refined 2q2u structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2Q2U 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 2Q2U

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 2Q2U, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2q2u_E] [2q2u_I] [2q2u_J] [2q2u_A] [2q2u_D] [2q2u_K] [2q2u_B] [2q2u_L] [2q2u_F] [2q2u_G] [2q2u_C] [2q2u_H] [2q2u] SWISS-PROT database: [O41026] Domain organization of [O41026_PBCV1] by SWISSPFAM

Other resources with information on 2Q2U

Community annotation for 2Q2U at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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