4PHA Transferase,Lyase Dna date May 05, 2014
title Structure Of Human Dna Polymerase Beta Complexed With A In T Template Base Paired With Incoming Non-Hydrolyzable Ctp
authors M.C.Koag, S.Lee
compound source
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: Enterobacteria Phage L1
Expression_system_taxid: 268588

Molecule: Dna (5'-D(Cpcpgpapcpaptpcpgpcpaptpcp 3');
Chain: T
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

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

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

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

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 1 21 1
R_factor 0.216 R_Free 0.278
crystal
cell
length a length b length c angle alpha angle beta angle gamma
54.440 80.710 54.834 90.00 108.88 90.00
method X-Ray Diffractionresolution 2.52 Å
ligand 0KX, MG, NA enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceThe spontaneous replication error and the mismatch discrimination mechanisms of human DNA polymerase beta, Koag MC, Nam K, Lee S, Nucleic Acids Res. 2014 Sep 8. pii: gku789. PMID:25200079
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (73 Kb) [Save to disk]
  • Biological Unit Coordinates (4pha.pdb1.gz) 68 Kb
  • LPC: Ligand-Protein Contacts for 4PHA
  • CSU: Contacts of Structural Units for 4PHA
  • Structure Factors (139 Kb)
  • Retrieve 4PHA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4PHA from S2C, [Save to disk]
  • Re-refined 4pha structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4PHA 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 4PHA
  • 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 4PHA, from MSDmotif at EBI
  • Fold representative 4pha from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4pha_T] [4pha_A] [4pha_P] [4pha_D] [4pha]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4PHA: [HhH1] [POLXc ] by SMART
  • Other resources with information on 4PHA
  • Community annotation for 4PHA at PDBWiki (http://pdbwiki.org)

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