4YMO Transferase Dna date Mar 07, 2015
title Structure Of Human Dna Polymerase Beta Complexed With N7bg I Template Opposite To Incoming Non-Hydrolyzable Ctp With Man 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 0.194 R_Free 0.226
crystal
cell
length a length b length c angle alpha angle beta angle gamma
50.728 79.170 55.634 90.00 107.23 90.00
method X-Ray Diffractionresolution 2.15 Å
ligand 0KX, 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] (76 Kb) [Save to disk]
  • Biological Unit Coordinates (4ymo.pdb1.gz) 71 Kb
  • LPC: Ligand-Protein Contacts for 4YMO
  • CSU: Contacts of Structural Units for 4YMO
  • Structure Factors (210 Kb)
  • Retrieve 4YMO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4YMO from S2C, [Save to disk]
  • Re-refined 4ymo structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4YMO 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 4YMO
  • 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 4ymo from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ymo_A] [4ymo_P] [4ymo_T] [4ymo_D] [4ymo]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4YMO: [HhH1] [POLXc ] by SMART
  • Other resources with information on 4YMO
  • Community annotation for 4YMO 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
    Bioinformatics Unit
    Weizmann Institute of Science