5TYE Transferase Dna date Nov 19, 2016
title Dna Polymerase Mu Product Complex, 10 Mm Mg2+ (60 Min)
authors J.A.Jamsen, S.H.Wilson
compound source
Molecule: Dna-Directed Dnarna Polymerase Mu
Chain: A
Fragment: Unp Residues 132-494
Synonym: Pol Mu,Terminal Transferase
Ec: 2.7.7.7
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Polm, Polmu
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: Codonplus-Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgexm

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

Synthetic: Yes
Organism_scientific: Unidentified
Organism_taxid: 32644

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

Synthetic: Yes
Organism_scientific: Unidentified
Organism_taxid: 32644

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

Synthetic: Yes
Organism_scientific: Unidentified
Organism_taxid: 32644
symmetry Space Group: P 21 21 21
R_factor 0.186 R_Free 0.228
crystal
cell
length a length b length c angle alpha angle beta angle gamma
59.998 68.573 110.478 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.05 Å
ligand DTT, EDO, EPE, MG, NA, PPV enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceTime-lapse crystallography snapshots of a double-strand break repair polymerase in action., Jamsen JA, Beard WA, Pedersen LC, Shock DD, Moon AF, Krahn JM, Bebenek K, Kunkel TA, Wilson SH, Nat Commun. 2017 Aug 15;8(1):253. doi: 10.1038/s41467-017-00271-7. PMID:28811466
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (77 Kb) [Save to disk]
  • Biological Unit Coordinates (5tye.pdb1.gz) 70 Kb
  • LPC: Ligand-Protein Contacts for 5TYE
  • CSU: Contacts of Structural Units for 5TYE
  • Structure Factors (767 Kb)
  • Retrieve 5TYE in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5TYE from S2C, [Save to disk]
  • View 5TYE 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 5TYE
  • 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 5tye from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5tye_A] [5tye_D] [5tye_P] [5tye_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5TYE
  • Community annotation for 5TYE at PDBWiki (http://pdbwiki.org)

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