5OMF Dna Binding Protein date Jul 31, 2017
title Closed, Ternary Structure Of Kod Dna Polymerase
authors H.M.Kropp, K.Betz, J.Wirth, K.Diederichs, A.Marx
compound source
Molecule: Dna Polymerase,Dna Polymerase,Dna Polymerase
Chain: A
Ec: 2.7.7.7,3.1.-.-,2.7.7.7,3.1.-.-,2.7.7.7,3.1.-.-
Engineered: Yes
Organism_scientific: Thermococcus Kodakarensis (Strain Atcc Jcm 12380 Kod1);
Organism_taxid: 69014
Gene: Pol, Tk0001
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'-D(Pcptpgptpgpgpcpcpgptpgpgpt
Chain: T
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Gpapcpcpapcpgpgpcpcpapc)-3'
Chain: P
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 21 21 2
R_factor 0.195 R_Free 0.234
crystal
cell
length a length b length c angle alpha angle beta angle gamma
107.909 147.559 71.142 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.09 Å
ligand DTP, EDO, GOL, MG, MN enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal structures of ternary complexes of archaeal B-family DNA polymerases., Kropp HM, Betz K, Wirth J, Diederichs K, Marx A, PLoS One. 2017 Dec 6;12(12):e0188005. doi: 10.1371/journal.pone.0188005., eCollection 2017. PMID:29211756
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (418 Kb) [Save to disk]
  • Biological Unit Coordinates (5omf.pdb1.gz) 410 Kb
  • LPC: Ligand-Protein Contacts for 5OMF
  • CSU: Contacts of Structural Units for 5OMF
  • Structure Factors (1546 Kb)
  • Retrieve 5OMF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5OMF from S2C, [Save to disk]
  • View 5OMF 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 5OMF
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5omf_A] [5omf_T] [5omf_P]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5OMF
  • Community annotation for 5OMF at PDBWiki (http://pdbwiki.org)

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