3L2P Ligase Dna date Dec 15, 2009
title Human Dna Ligase III Recognizes Dna Ends By Dynamic Switchin Two Dna Bound States
authors E.A.Cotner-Gohara, I.K.Kim, M.Hammel, J.A.Tainer, A.Tomkinson, T.Ellenberger
compound source
Molecule: Dna Ligase 3
Chain: A
Fragment: Unp Residues 257-833
Synonym: Dna Ligase III, Polydeoxyribonucleotide Synthase [
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Lig3
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Pet-28

Molecule: 5'-D(Pcpgpgpgpaptpgpcpgptpc)-3'
Chain: B
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Construct

Molecule: 5'-D(Gptpcpgpgpapcptpg)-3'
Chain: C
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Construct

Molecule: 5'-D(Gpcpcpapgptpcpcpgpapcpgpapcpg Cpcpcpg)-3';
Chain: D
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Construct
symmetry Space Group: P 41 21 2
R_factor 0.233 R_Free 0.271
length a length b length c angle alpha angle beta angle gamma
130.149 130.149 150.431 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.00 Å
ligand AMP enzyme Ligase E.C. BRENDA

Primary referenceHuman DNA Ligase III Recognizes DNA Ends by Dynamic Switching Between Two DNA Bound States., Cotner-Gohara E, Kim IK, Hammel M, Tainer JA, Tomkinson AE, Ellenberger T, Biochemistry. 2010 Jun 2. PMID:20518483
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (221 Kb) [Save to disk]
  • Biological Unit Coordinates (3l2p.pdb1.gz) 214 Kb
  • LPC: Ligand-Protein Contacts for 3L2P
  • CSU: Contacts of Structural Units for 3L2P
  • Structure Factors (202 Kb)
  • Retrieve 3L2P in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3L2P from S2C, [Save to disk]
  • Re-refined 3l2p structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3L2P 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 3L2P
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3L2P, from MSDmotif at EBI
  • Fold representative 3l2p from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3l2p_B] [3l2p_D] [3l2p] [3l2p_C] [3l2p_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3L2P
  • Community annotation for 3L2P at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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