2KFZ Transferase Dna date Jul 02, 1998
title Klenow Fragment With Bridging-Sulfur Substrate And Zinc Only
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
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 0.215 R_Free 0.255
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, US1, ZN enzyme Transferase E.C. BRENDA
related structures by homologous chain: 1D8Y, 2KFN

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] (110 Kb) [Save to disk]
  • Biological Unit Coordinates (2kfz.pdb1.gz) 104 Kb
  • LPC: Ligand-Protein Contacts for 2KFZ
  • CSU: Contacts of Structural Units for 2KFZ
  • Likely Quarternary Molecular Structure file(s) for 2KFZ
  • Structure Factors (466 Kb)
  • Retrieve 2KFZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2KFZ from S2C, [Save to disk]
  • Re-refined 2kfz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2KFZ 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 2KFZ
  • 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 2KFZ, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d2kfza1, region A:324-518 [Jmol] [rasmolscript] [script source]
        - Domain d2kfza2, region A:519-928 [Jmol] [rasmolscript] [script source]
  • Fold representative 2kfz 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: [2kfz_A] [2kfz_B] [2kfz]
  • SWISS-PROT database: [P00582]
  • Domain organization of [DPO1_ECOLI] by SWISSPFAM
  • Domains found in 2KFZ: [35EXOc] [POLAc ] by SMART
  • Other resources with information on 2KFZ
  • Community annotation for 2KFZ at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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