1XSP Transferase Dna date Oct 19, 2004
title Crystal Structure Of Human Dna Polymerase Lambda In Complex Nicked Dna And Pyrophosphate
authors M.Garcia-Diaz, K.Bebenek, J.M.Krahn, T.A.Kunkel, L.C.Pedersen
compound source
Molecule: 5'-D(Cpgpgpcpcpgptpapcptpg)-3'
Chain: T
Engineered: Yes
Synthetic: Yes
Other_details: Template Dna

Molecule: 5'-D(Cpapgptpapcpg)-3'
Chain: P
Engineered: Yes

Synthetic: Yes
Other_details: Primer Dna

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

Synthetic: Yes
Other_details: Downstream Primer Dna

Molecule: Dna Polymerase Lambda
Chain: A
Fragment: 39 Kda Catalytic C-Terminal Domain
Synonym: Pol Lambda, Dna Polymerase Beta-2, Pol Beta2
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Poll
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22-B
symmetry Space Group: P 21 21 21
R_factor 0.206 R_Free 0.242
length a length b length c angle alpha angle beta angle gamma
55.845 62.758 140.720 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand NA, PPV enzyme Transferase E.C. BRENDA
related structures by homologous chain: 1RZT, 1XSL

Primary referenceA closed conformation for the Pol lambda catalytic cycle., Garcia-Diaz M, Bebenek K, Krahn JM, Kunkel TA, Pedersen LC, Nat Struct Mol Biol. 2005 Jan;12(1):97-8. Epub 2004 Dec 19. PMID:15608652
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (73 Kb) [Save to disk]
  • Biological Unit Coordinates (1xsp.pdb1.gz) 68 Kb
  • LPC: Ligand-Protein Contacts for 1XSP
  • CSU: Contacts of Structural Units for 1XSP
  • Likely Quarternary Molecular Structure file(s) for 1XSP
  • Structure Factors (326 Kb)
  • Retrieve 1XSP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1XSP from S2C, [Save to disk]
  • Re-refined 1xsp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1XSP 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 1XSP
  • 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 1XSP, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1xsp_D] [1xsp_A] [1xsp_P] [1xsp] [1xsp_T]
  • SWISS-PROT database: [Q9UGP5]
  • Domain organization of [DPOLL_HUMAN] by SWISSPFAM
  • Domains found in 1XSP: [HhH1] [POLXc ] by SMART
  • Other resources with information on 1XSP
  • Community annotation for 1XSP 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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