5U8G Transferase,Lyase Dna date Dec 14, 2016
title Dna Polymerase Beta Crystallized In Peg 400
authors B.E.Eckenroth, S.Doublie
compound source
Molecule: Dna Polymerase Beta
Chain: A
Fragment: Dna Polymerase
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Polb
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta 2 De3
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a

Molecule: Dna (5'-D(Cpcpgpapcpapgpcpgpcpaptpcp 3');
Chain: T
Engineered: Yes
Other_details: Dna Template Strand

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Dna Primer Strand, 10mer

Molecule: Dna (5'-D(Gpcptpgpaptpgpcpgpc)-3')
Chain: P
Engineered: Yes
Other_details: Dna Primer Strand

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Dna Downstream Strand, 5mer

Molecule: Dna (5'-D(Gptpcpgpg)-3')
Chain: D
Engineered: Yes
Other_details: Dna Downstream Strand

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 1 21 1
R_factor 0.179 R_Free 0.225
length a length b length c angle alpha angle beta angle gamma
54.104 78.659 54.721 90.00 104.25 90.00
method X-Ray Diffractionresolution 2.17 Å
ligand CL, NA enzyme Transferase E.C. BRENDA

Primary referenceRemote Mutations Induce Functional Changes in Active Site Residues of Human DNA Polymerase beta., Eckenroth BE, Towle-Weicksel JB, Nemec AA, Murphy DL, Sweasy JB, Doublie S, Biochemistry. 2017 Apr 21. doi: 10.1021/acs.biochem.6b01287. PMID:28402631
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (142 Kb) [Save to disk]
  • Biological Unit Coordinates (5u8g.pdb1.gz) 135 Kb
  • LPC: Ligand-Protein Contacts for 5U8G
  • CSU: Contacts of Structural Units for 5U8G
  • Structure Factors (1191 Kb)
  • Retrieve 5U8G in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5U8G from S2C, [Save to disk]
  • Re-refined 5u8g structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5U8G 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 5U8G
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5u8g from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5u8g_D] [5u8g_A] [5u8g_P] [5u8g] [5u8g_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5U8G
  • Community annotation for 5U8G at PDBWiki (http://pdbwiki.org)

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