5KFC Replication, Transferase Dna date Jun 12, 2016
title Human Dna Polymerase Eta-Dna Ternary Complex: Reaction With For 180s
authors Y.Gao, W.Yang
compound source
Molecule: Dna Polymerase Eta
Chain: A
Synonym: Rad30 Homolog A,Xeroderma Pigmentosum Variant Type
Ec: 2.7.7.7
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Polh, Rad30, Rad30a, Xpv
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28

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

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

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

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
symmetry Space Group: P 61
R_factor 0.180 R_Free 0.210
crystal
cell
length a length b length c angle alpha angle beta angle gamma
98.150 98.150 82.090 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.50 Å
ligand CA, DTP, GOL, MN enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCapture of a third Mg(2)(+) is essential for catalyzing DNA synthesis., Gao Y, Yang W, Science. 2016 Jun 10;352(6291):1334-7. doi: 10.1126/science.aad9633. PMID:27284197
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (94 Kb) [Save to disk]
  • Biological Unit Coordinates (5kfc.pdb1.gz) 89 Kb
  • LPC: Ligand-Protein Contacts for 5KFC
  • CSU: Contacts of Structural Units for 5KFC
  • Structure Factors (1195 Kb)
  • Retrieve 5KFC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5KFC from S2C, [Save to disk]
  • Re-refined 5kfc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5KFC 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 5KFC
  • 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 5kfc from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5kfc_P] [5kfc_A] [5kfc] [5kfc_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5KFC
  • Community annotation for 5KFC at PDBWiki (http://pdbwiki.org)

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