4KHN Hydrolase, Transferase Dna date Apr 30, 2013
title Crystal Structure Of The Ternary Complex Of The D714a Mutant Dna Polymerase
authors K.E.Guja, A.Jacewicz, A.Trzemecka, D.Plochocka, E.Yakubovskaya, A M.Garcia-Diaz
compound source
Molecule: Dna Polymerase
Chain: A, B
Synonym: Gp43
Engineered: Yes
Mutation: Yes
Organism_scientific: Enterobacteria Phage Rb69
Organism_taxid: 12353
Gene: 43
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'- D(Tpcpapcpgptpapapgpcpapgptpcpcpgpcpg)-3'
Chain: C, E
Engineered: Yes

Synthetic: Yes

Molecule: Dna (5'-D(Gpcpgpgpapcptpgpcptptpapc)
Chain: D, F
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 1 21 1
R_factor 0.168 R_Free 0.211
length a length b length c angle alpha angle beta angle gamma
74.258 119.353 148.031 90.00 91.64 90.00
method X-Ray Diffractionresolution 2.55 Å
ligand CA, GOL, NA, SO4, XG4 enzyme Transferase E.C. BRENDA
A, B
  • DNA-directed DNA polymerase ...
  • nuclease activity
  • exonuclease activity
  • 3'-5' exonuclease activity

  • Primary referenceA Remote Palm Domain Residue of RB69 DNA Polymerase Is Critical for Enzyme Activity and Influences the Conformation of the Active Site., Jacewicz A, Trzemecka A, Guja KE, Plochocka D, Yakubovskaya E, Bebenek A, Garcia-Diaz M, PLoS One. 2013 Oct 7;8(10):e76700. doi: 10.1371/journal.pone.0076700. PMID:24116139
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (663 Kb) [Save to disk]
  • Biological Unit Coordinates (4khn.pdb1.gz) 337 Kb
  • Biological Unit Coordinates (4khn.pdb2.gz) 320 Kb
  • LPC: Ligand-Protein Contacts for 4KHN
  • CSU: Contacts of Structural Units for 4KHN
  • Structure Factors (769 Kb)
  • Retrieve 4KHN in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4KHN from S2C, [Save to disk]
  • Re-refined 4khn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4KHN 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 4KHN
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4KHN, from MSDmotif at EBI
  • Fold representative 4khn from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4khn_C] [4khn] [4khn_A] [4khn_B] [4khn_F] [4khn_E] [4khn_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4KHN: [POLBc ] by SMART
  • Other resources with information on 4KHN
  • Community annotation for 4KHN at PDBWiki (http://pdbwiki.org)

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