2HVR	Ligase Rna Dna	date	Jul 30, 2006
title	Structure Of T4 Rna Ligase 2 With Nicked 5'-Adenylated Nucle Duplex Containing A 3'-Deoxyribonucleotide At The Nick
authors	J.Nandakumar, C.D.Lima
compound		source
Molecule: 5'-D(Aptptpcpcpgpaptpapgptpgpgpgpg Cpapaptptpg)-3'; Chain: C, F Engineered: Yes		Synthetic: Yes
Molecule: 5'-D(Cpapaptptpgpcpgpapc)-R(P(Omc)Pc) Chain: D, G Engineered: Yes		Synthetic: Yes
Molecule: 5'-R(Pa)-D(Pcpapcptpaptpcpgpgpapapt) Chain: E, H Engineered: Yes		Synthetic: Yes
Molecule: T4 Rna Ligase 2 Chain: A, B Engineered: Yes		Organism_scientific: Enterobacteria Phage T4 Organism_taxid: 10665 Gene: Y10a, 24.1 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet-His-Smt3-Rnl2
symmetry	Space Group: P 21 21 21	R_factor 0.236 R_Free 0.295
crystal cell	length a length b length c angle alpha angle beta angle gamma 83.569 106.160 125.329 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.45 Å
ligand	BTB, O2C, OMC	enzyme
Gene Ontology	Chain Function Process Component A, B
Primary reference	RNA Ligase Structures Reveal the Basis for RNA Specificity and Conformational Changes that Drive Ligation Forward., Nandakumar J, Shuman S, Lima CD, Cell. 2006 Oct 6;127(1):71-84. PMID:17018278

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (152 Kb) [Save to disk] Biological Unit Coordinates (2hvr.pdb1.gz) 74 Kb Biological Unit Coordinates (2hvr.pdb2.gz) 73 Kb LPC: Ligand-Protein Contacts for 2HVR CSU: Contacts of Structural Units for 2HVR Likely Quarternary Molecular Structure file(s) for 2HVR Structure Factors (348 Kb) Retrieve 2HVR in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2HVR from S2C, [Save to disk] Re-refined 2hvr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2HVR 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 2HVR

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 2HVR, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2hvr_G] [2hvr_C] [2hvr_A] [2hvr_D] [2hvr_B] [2hvr_E] [2hvr_F] [2hvr] [2hvr_H] SWISS-PROT database: [P32277] Domain organization of [RLIG2_BPT4] by SWISSPFAM

Other resources with information on 2HVR

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

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