5C53 Transferase Dna date Jun 19, 2015
title Probing The Structural And Molecular Basis Of Nucleotide Sel By Human Mitochondrial Dna Polymerase Gamma
authors C.D.Sohl, M.R.Szymanski, A.C.Mislak, C.K.Shumate, S.Amiralaei, R.F.Schinazi, K.S.Anderson, Y.W.Yin
compound source
Molecule: Dna Polymerase Subunit Gamma-1
Chain: A
Synonym: Mitochondrial Dna Polymerase Catalytic Subunit,Pol
Ec: 2.7.7.7
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Polg, Mdp1, Polg1, Polga
Expression_system: Insect Cell Expression Vector Ptie1
Expression_system_taxid: 266783

Molecule: Pol Gamma B
Chain: B, C
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Expression_system: Insect Cell Expression Vector Ptie1
Expression_system_taxid: 266783

Molecule: Dna (26-Mer)
Chain: T
Engineered: Yes

Synthetic: Yes
Organism_scientific: Dna Launch Vector Pde-Gfp2
Organism_taxid: 415098

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

Synthetic: Yes
Organism_scientific: Dna Launch Vector Pde-Gfp2
Organism_taxid: 415098
symmetry Space Group: P 41 21 2
R_factor 0.300 R_Free 0.338
crystal
cell
length a length b length c angle alpha angle beta angle gamma
217.447 217.447 163.593 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.57 Å
ligand 4Y3, DOC, MG enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A
  • DNA-directed DNA polymerase ...
  • 3'-5' exonuclease activity
  • cellular response to glucose...

  • C, B


    Primary referenceProbing the structural and molecular basis of nucleotide selectivity by human mitochondrial DNA polymerase gamma., Sohl CD, Szymanski MR, Mislak AC, Shumate CK, Amiralaei S, Schinazi RF, Anderson KS, Yin YW, Proc Natl Acad Sci U S A. 2015 Jul 14;112(28):8596-601. doi:, 10.1073/pnas.1421733112. Epub 2015 Jun 29. PMID:26124101
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (314 Kb) [Save to disk]
  • Biological Unit Coordinates (5c53.pdb1.gz) 298 Kb
  • LPC: Ligand-Protein Contacts for 5C53
  • CSU: Contacts of Structural Units for 5C53
  • Structure Factors (376 Kb)
  • Retrieve 5C53 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5C53 from S2C, [Save to disk]
  • Re-refined 5c53 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5C53 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 5C53
  • 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 5c53 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5c53_T] [5c53] [5c53_B] [5c53_P] [5c53_A] [5c53_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5C53: [POLAc ] by SMART
  • Other resources with information on 5C53
  • Community annotation for 5C53 at PDBWiki (http://pdbwiki.org)

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science