1D8Y Transferase Dna date Oct 26, 1999
title Crystal Structure Of The Complex Of Dna Polymerase I Klenow With Dna
authors M.Teplova, S.T.Wallace, V.Tereshko, G.Minasov, A.M.Simons, P.D.Co M.Manoharan, M.Egli
compound source
Molecule: D(T)19 Oligomer
Chain: B
Engineered: Yes
Synthetic: Yes

Molecule: Dna Polymerase I
Chain: A
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
symmetry Space Group: P 43
R_factor 0.217 R_Free 0.233
length a length b length c angle alpha angle beta angle gamma
101.880 101.880 85.180 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.08 Å
ligand SO4, ZN enzyme Transferase E.C. BRENDA
related structures by homologous chain: 1KFS, 2KFZ

Primary referenceStructural origins of the exonuclease resistance of a zwitterionic RNA., Teplova M, Wallace ST, Tereshko V, Minasov G, Symons AM, Cook PD, Manoharan M, Egli M, Proc Natl Acad Sci U S A 1999 Dec 7;96(25):14240-5. PMID:10588690
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (109 Kb) [Save to disk]
  • Biological Unit Coordinates (1d8y.pdb1.gz) 102 Kb
  • LPC: Ligand-Protein Contacts for 1D8Y
  • CSU: Contacts of Structural Units for 1D8Y
  • Likely Quarternary Molecular Structure file(s) for 1D8Y
  • Structure Factors (368 Kb)
  • Retrieve 1D8Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1D8Y from S2C, [Save to disk]
  • Re-refined 1d8y structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1D8Y 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 1D8Y
  • 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 1D8Y, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1d8ya1, region A:324-518 [Jmol] [rasmolscript] [script source]
        - Domain d1d8ya2, region A:519-928 [Jmol] [rasmolscript] [script source]
  • Fold representative 1d8y 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: [1d8y_B] [1d8y] [1d8y_A]
  • SWISS-PROT database: [P00582]
  • Domain organization of [DPO1_ECOLI] by SWISSPFAM
  • Domains found in 1D8Y: [35EXOc] [POLAc ] by SMART
  • Other resources with information on 1D8Y
  • Community annotation for 1D8Y 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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