4YN4 Transferase Dna date Mar 09, 2015
title Structure Of Human Dna Polymerase Beta Complexed With N7bg I Template Opposite To Incoming Non-Hydrolyzable Dttp With Ma The Active Site
authors S.Lee, M.C.Koag
compound source
Molecule: Dna Polymerase Beta
Chain: A
Ec: 2.7.7.7,4.2.99.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Polb
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna 16-Mer (Template)
Chain: T
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Dna 10-Mer (Up-Primer)
Chain: P
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Dna 5-Mer (Dn-Primer)
Chain: D
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 1 21 1
R_factor 0.203 R_Free 0.255
crystal
cell
length a length b length c angle alpha angle beta angle gamma
54.774 79.179 55.031 90.00 106.53 90.00
method X-Ray Diffractionresolution 2.24 Å
ligand 1FZ, 7BG, MN, NA enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural and kinetic studies of the effect of guanine-N7 alkylation and metal cofactors on DNA replication., Kou Y, Koag MC, Lee S, Biochemistry. 2018 Jun 29. doi: 10.1021/acs.biochem.8b00331. PMID:29957995
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (75 Kb) [Save to disk]
  • Biological Unit Coordinates (4yn4.pdb1.gz) 70 Kb
  • LPC: Ligand-Protein Contacts for 4YN4
  • CSU: Contacts of Structural Units for 4YN4
  • Structure Factors (197 Kb)
  • Retrieve 4YN4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4YN4 from S2C, [Save to disk]
  • Re-refined 4yn4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4YN4 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 4YN4
  • 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 4yn4 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4yn4] [4yn4_P] [4yn4_A] [4yn4_D] [4yn4_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4YN4: [HhH1] [POLXc ] by SMART
  • Other resources with information on 4YN4
  • Community annotation for 4YN4 at PDBWiki (http://pdbwiki.org)

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