5VBN Transferase date Mar 29, 2017
title Crystal Structure Of Human Dna Polymerase Epsilon B-Subunit With C-Terminal Domain Of Catalytic Subunit
authors A.G.Baranovskiy, J.Gu, Y.Suwa, N.D.Babayeva, T.H.Tahirov
compound source
Molecule: Dna Polymerase Epsilon Subunit 2
Chain: A, E
Synonym: Dna Polymerase II Subunit 2,Dna Polymerase Epsilon B;
Ec: 2.7.7.7
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pole2, Dpe2
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna Polymerase Epsilon Catalytic Subunit A
Chain: B, F
Fragment: Unp Residues 2142-2286
Synonym: Dna Polymerase II Subunit A
Ec: 2.7.7.7
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pole, Pole1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 2
R_factor 0.225 R_Free 0.264
crystal
cell
length a length b length c angle alpha angle beta angle gamma
92.260 201.459 78.336 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.35 Å
ligand SO4, ZN enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, E


F, B


Primary referenceCrystal structure of the human Pol B-subunit in complex with the C-terminal domain of the catalytic subunit., Baranovskiy AG, Gu J, Babayeva ND, Kurinov I, Pavlov YI, Tahirov TH, J Biol Chem. 2017 Jul 26. pii: jbc.M117.792705. doi: 10.1074/jbc.M117.792705. PMID:28747437
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (186 Kb) [Save to disk]
  • Biological Unit Coordinates (5vbn.pdb1.gz) 92 Kb
  • Biological Unit Coordinates (5vbn.pdb2.gz) 91 Kb
  • LPC: Ligand-Protein Contacts for 5VBN
  • CSU: Contacts of Structural Units for 5VBN
  • Structure Factors (587 Kb)
  • Retrieve 5VBN in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5VBN from S2C, [Save to disk]
  • Re-refined 5vbn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5VBN 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 5VBN
  • 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
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5vbn_F] [5vbn_A] [5vbn_E] [5vbn_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5VBN
  • Community annotation for 5VBN at PDBWiki (http://pdbwiki.org)

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