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 Diffraction	resolution	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	Chain Function Process Component A
Primary reference	Structures 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] (109 Kb) [Save to disk] Biological Unit Coordinates (2kfn.pdb1.gz) 104 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

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 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] 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)

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