2KFN Transferase Dna date Jul 01, 1998
title Klenow Fragment With Bridging-Sulfur Substrate And Manganese
authors C.A.Brautigam, S.Sun, J.A.Piccirilli, T.A.Steitz
compound source
Molecule: 5'-D(Gpcptptpap(Us1)Pg)-3'
Chain: B
Engineered: Yes
Synthetic: Yes

Molecule: Klenow Fragment Of Dna Polymerase I
Chain: A
Fragment: Large Fragment, Klenow Fragment
Synonym: Pol I, Dna-Directed Dna Polymerase
Ec: 2.7.7.7
Engineered: Yes
Mutation: Yes

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Cj376
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcj155
symmetry Space Group: P 43
R_factor 0.214 R_Free 0.250
crystal
cell
length a length b length c angle alpha angle beta angle gamma
102.900 102.900 86.400 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.03 Å
ligand MG, MN, US1, ZN enzyme Transferase E.C.2.7.7.7 BRENDA
related structures by homologous chain: 2KFZ
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructures of normal single-stranded DNA and deoxyribo-3'-S-phosphorothiolates bound to the 3'-5' exonucleolytic active site of DNA polymerase I from Escherichia coli., Brautigam CA, Sun S, Piccirilli JA, Steitz TA, Biochemistry 1999 Jan 12;38(2):696-704. PMID:9888810
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (111 Kb) [Save to disk]
  • Biological Unit Coordinates (2kfn.pdb1.gz) 106 Kb
  • LPC: Ligand-Protein Contacts for 2KFN
  • CSU: Contacts of Structural Units for 2KFN
  • Likely Quarternary Molecular Structure file(s) for 2KFN
  • Structure Factors (468 Kb)
  • Retrieve 2KFN in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2KFN from S2C, [Save to disk]
  • Re-refined 2kfn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2KFN 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 2KFN
  • 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 2KFN, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d2kfna1, region A:324-518 [Jmol] [rasmolscript] [script source]
        - Domain d2kfna2, region A:519-928 [Jmol] [rasmolscript] [script source]
  • Fold representative 2kfn from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2kfn_B] [2kfn_A] [2kfn]
  • SWISS-PROT database: [P00582]
  • Domain organization of [DPO1_ECOLI] by SWISSPFAM
  • Domains found in 2KFN: [35EXOc] [POLAc ] by SMART
  • Other resources with information on 2KFN
  • Community annotation for 2KFN at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • 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