1ZJM Dna Lyase Transferase date Apr 29, 2005
title Human Dna Polymerase Beta Complexed With Dna Containing An A-A Mismatched Primer Terminus
authors V.K.Batra, W.A.Beard, D.D.Shock, L.C.Pedersen, S.H.Wilson
compound source
Molecule: D(Cpcpgpapcpcpapcpgpcpaptpcpapgpc )-3';
Chain: T
Engineered: Yes
Synthetic: Yes

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

Synthetic: Yes

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

Synthetic: Yes

Molecule: Dna Polymerase Beta
Chain: A
Ec: 2.7.7.7, 4.2.99.-
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Polb
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.228 R_Free 0.234
crystal
cell
length a length b length c angle alpha angle beta angle gamma
54.100 79.100 54.900 90.00 105.90 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand NA enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceNucleotide-induced DNA polymerase active site motions accommodating a mutagenic DNA intermediate., Batra VK, Beard WA, Shock DD, Pedersen LC, Wilson SH, Structure (Camb) 2005 Aug;13(8):1225-33. PMID:16084394
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (77 Kb) [Save to disk]
  • Biological Unit Coordinates (1zjm.pdb1.gz) 72 Kb
  • LPC: Ligand-Protein Contacts for 1ZJM
  • CSU: Contacts of Structural Units for 1ZJM
  • Likely Quarternary Molecular Structure file(s) for 1ZJM
  • Structure Factors (357 Kb)
  • Retrieve 1ZJM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1ZJM from S2C, [Save to disk]
  • Re-refined 1zjm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1ZJM 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 1ZJM
  • 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 1ZJM, from MSDmotif at EBI
  • Fold representative 1zjm from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1zjm_P] [1zjm_D] [1zjm_A] [1zjm_T] [1zjm]
  • SWISS-PROT database: [P06746]
  • Domain organization of [DPOLB_HUMAN] by SWISSPFAM
  • Domains found in 1ZJM: [HhH1] [POLXc ] by SMART
  • Other resources with information on 1ZJM
  • Community annotation for 1ZJM 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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