2ISP Transferase Dna date Oct 18, 2006
title Ternary Complex Of Dna Polymerase Beta With A Dideoxy Terminated Primer And 2'-Deoxyguanosine 5'-Beta, Gamma- Methylene Triphosphate
authors C.A.Sucato, T.G.Upton, B.A.Kashemirov, V.Martinek, Y.Xiang, W.A.Beard
compound source
Molecule: 5'- D(Cpcpgpapcpcpgpcpgpcpaptpcpapgpc)-3';
Chain: T
Engineered: Yes
Synthetic: Yes

Molecule: 5'-D(Gpcptpgpaptpgpcpgp(Doc))-3'
Chain: P
Engineered: Yes

Synthetic: Yes

Molecule: 5'-D(Pgptpcpgpg)-3'
Chain: D
Engineered: Yes

Synthetic: Yes

Molecule: Polymerase (Dna Directed), Beta
Chain: A
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Polb
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.201 R_Free 0.261
length a length b length c angle alpha angle beta angle gamma
50.700 80.400 55.500 90.00 107.90 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand CL, DOC, GGH, MG, NA enzyme Transferase E.C. BRENDA

Primary referenceModifying the beta,gamma Leaving-Group Bridging Oxygen Alters Nucleotide Incorporation Efficiency, Fidelity, and the Catalytic Mechanism of DNA Polymerase beta., Sucato CA, Upton TG, Kashemirov BA, Batra VK, Martinek V, Xiang Y, Beard WA, Pedersen LC, Wilson SH, McKenna CE, Florian J, Warshel A, Goodman MF, Biochemistry. 2007 Jan 16;46(2):461-471. PMID:17209556
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (79 Kb) [Save to disk]
  • Biological Unit Coordinates (2isp.pdb1.gz) 74 Kb
  • LPC: Ligand-Protein Contacts for 2ISP
  • CSU: Contacts of Structural Units for 2ISP
  • Likely Quarternary Molecular Structure file(s) for 2ISP
  • Structure Factors (284 Kb)
  • Retrieve 2ISP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2ISP from S2C, [Save to disk]
  • Re-refined 2isp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2ISP 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 2ISP
  • 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 2ISP, from MSDmotif at EBI
  • Fold representative 2isp from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2isp_P] [2isp_T] [2isp] [2isp_A] [2isp_D]
  • SWISS-PROT database: [P06746]
  • Domain organization of [DPOLB_HUMAN] by SWISSPFAM
  • Domains found in 2ISP: [HhH1] [POLXc ] by SMART
  • Other resources with information on 2ISP
  • Community annotation for 2ISP 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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