2CFM	Ligase	date	Feb 22, 2006
title	Atp-Dependent Dna Ligase From Pyrococcus Furiosus
authors	H.Nishida, Y.Ishino, K.Morikawa
compound		source
Molecule: Thermostable Dna Ligase Chain: A Synonym: Polydeoxyribonucleotide Synthase [Atp], Pfu Dna Li Ec: 6.5.1.1 Engineered: Yes Other_details: Amp Is Bound In The Pocket Non-Covalently		Organism_scientific: Pyrococcus Furiosus Organism_taxid: 2261 Expression_system: Escherichia Coli Expression_system_taxid: 511693 Expression_system_strain: Bl21 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet21d
symmetry	Space Group: P 1 21 1	R_factor 0.204 R_Free 0.231
crystal cell	length a length b length c angle alpha angle beta angle gamma 60.866 87.399 62.648 90.00 109.22 90.00
method	X-Ray Diffraction	resolution	1.80 Å
ligand	AMP, MG, MSE	enzyme	Ligase E.C.6.5.1.1 BRENDA
Gene Ontology	Chain Function Process Component A
Primary reference	The closed structure of an archaeal DNA ligase from Pyrococcus furiosus., Nishida H, Kiyonari S, Ishino Y, Morikawa K, J Mol Biol. 2006 Jul 28;360(5):956-67. Epub 2006 Jun 12. PMID:16820169

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (105 Kb) [Save to disk] Biological Unit Coordinates (2cfm.pdb1.gz) 100 Kb LPC: Ligand-Protein Contacts for 2CFM CSU: Contacts of Structural Units for 2CFM Likely Quarternary Molecular Structure file(s) for 2CFM Structure Factors (457 Kb) Retrieve 2CFM in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2CFM from S2C, [Save to disk] Re-refined 2cfm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2CFM 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 2CFM

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 2CFM, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2cfm_A] [2cfm] SWISS-PROT database: [P56709] Domain organization of [DNLI_PYRFU] by SWISSPFAM

Other resources with information on 2CFM

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

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