5VZC Transferase Dna date May 27, 2017
title Post-Catalytic Complex Of Human Polymerase Mu (G433s) Mutant Incoming Dttp
authors A.F.Moon, J.M.Pryor, D.A.Ramsden, T.A.Kunkel, K.Bebenek, L.C.Pede
compound source
Molecule: Dna-Directed Dnarna Polymerase Mu
Chain: A
Fragment: Residues 134-494
Synonym: Pol Mu,Terminal Transferase
Ec: 2.7.7.7
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Polm, Polmu
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgexm

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

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

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

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

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

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 21 21 21
R_factor 0.165 R_Free 0.190
crystal
cell
length a length b length c angle alpha angle beta angle gamma
60.112 68.716 110.993 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.55 Å
ligand CL, EDO, GOL, MG, NA, TTP enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural accommodation of ribonucleotide incorporation by the DNA repair enzyme polymerase Mu., Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K, Pedersen LC, Nucleic Acids Res. 2017 Sep 6;45(15):9138-9148. doi: 10.1093/nar/gkx527. PMID:28911097
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (138 Kb) [Save to disk]
  • Biological Unit Coordinates (5vzc.pdb1.gz) 131 Kb
  • LPC: Ligand-Protein Contacts for 5VZC
  • CSU: Contacts of Structural Units for 5VZC
  • Structure Factors (559 Kb)
  • Retrieve 5VZC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5VZC from S2C, [Save to disk]
  • Re-refined 5vzc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5VZC 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 5VZC
  • 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
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5vzc_P] [5vzc_D] [5vzc_T] [5vzc_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5VZC
  • Community annotation for 5VZC 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, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science