4Q5V Transferase Dna Rna date Apr 17, 2014
title Crystal Structure Of The Catalytic Core Of Human Dna Polymer In Ternary Complex With An Rna-Primed Dna Template And Aphi
authors A.G.Baranovskiy, N.D.Babayeva, Y.Suwa, J.Gu, T.H.Tahirov
compound source
Molecule: Dna Polymerase Alpha Catalytic Subunit
Chain: A, E
Fragment: Human Dna Polymerase Apha Catalytic Core Domain R 336-1257;
Synonym: Dna Polymerase Alpha Catalytic Subunit P180
Ec: 2.7.7.7
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pola1, Pola
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
Expression_system_strain: Sf-21
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pfastbac1

Molecule: Rna Primer
Chain: B, F
Engineered: Yes

Synthetic: Yes

Molecule: Dna Template
Chain: C, G
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 21 21 21
R_factor 0.233 R_Free 0.268
crystal
cell
length a length b length c angle alpha angle beta angle gamma
105.051 116.432 233.026 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.52 Å
ligand 2ZE enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, E


Primary referenceStructural basis for inhibition of DNA replication by aphidicolin., Baranovskiy AG, Babayeva ND, Suwa Y, Gu J, Pavlov YI, Tahirov TH, Nucleic Acids Res. 2014 Nov 27. pii: gku1209. PMID:25429975
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (313 Kb) [Save to disk]
  • Biological Unit Coordinates (4q5v.pdb1.gz) 156 Kb
  • Biological Unit Coordinates (4q5v.pdb2.gz) 154 Kb
  • LPC: Ligand-Protein Contacts for 4Q5V
  • CSU: Contacts of Structural Units for 4Q5V
  • Structure Factors (1127 Kb)
  • Retrieve 4Q5V in mmCIF format [Save to disk]
  • Re-refined 4q5v structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4Q5V 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 4Q5V
  • 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
  • 3D motif for 4Q5V, from MSDmotif at EBI
  • Fold representative 4q5v from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4q5v_A] [4q5v_G] [4q5v_E] [4q5v] [4q5v_C] [4q5v_B] [4q5v_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4Q5V: [POLBc ] by SMART
  • Other resources with information on 4Q5V
  • Community annotation for 4Q5V at PDBWiki (http://pdbwiki.org)

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