5VZD Transferase Dna date May 27, 2017
title Pre-Catalytic Ternary Complex Of Human Polymerase Mu (W434a) With Incoming Nonhydrolyzable Umpnpp
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: Unp 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(Cpgptpa)-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 0.166 R_Free 0.183
crystal
cell
length a length b length c angle alpha angle beta angle gamma
59.818 68.841 109.855 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.60 Å
ligand
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] (143 Kb) [Save to disk]
  • Biological Unit Coordinates (5vzd.pdb1.gz) 136 Kb
  • CSU: Contacts of Structural Units for 5VZD
  • Structure Factors (548 Kb)
  • Retrieve 5VZD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5VZD from S2C, [Save to disk]
  • Re-refined 5vzd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5VZD 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 5VZD
  • 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
  • Fold representative 5vzd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5vzd_D] [5vzd_T] [5vzd_A] [5vzd_P]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5VZD
  • Community annotation for 5VZD at PDBWiki (http://pdbwiki.org)

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