1TV9 Transferase Dna date Jun 29, 2004
title Human Dna Polymerase Beta Complexed With Nicked Dna Containing A Mismatched Template Adenine And Incoming Cytidine
authors J.M.Krahn, W.M.Beard, S.H.Wilson
compound source
Molecule: 5'- D(Cpcpgpapcpapgpcpgpcpaptpcpapgpc)-3';
Chain: T
Engineered: Yes
Synthetic: Yes

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

Synthetic: Yes

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

Synthetic: Yes

Molecule: Dna Polymerase Beta
Chain: A
Ec: 2.7.7.7
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 0.179 R_Free 0.239
crystal
cell
length a length b length c angle alpha angle beta angle gamma
54.680 79.650 54.670 90.00 106.77 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand MG, NA, PO4 enzyme Transferase E.C.2.7.7.7 BRENDA
related structures by homologous chain: 1BPY
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural insights into DNA polymerase beta deterrents for misincorporation support an induced-fit mechanism for fidelity., Krahn JM, Beard WA, Wilson SH, Structure (Camb) 2004 Oct;12(10):1823-32. PMID:15458631
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (89 Kb) [Save to disk]
  • Biological Unit Coordinates (1tv9.pdb1.gz) 84 Kb
  • LPC: Ligand-Protein Contacts for 1TV9
  • CSU: Contacts of Structural Units for 1TV9
  • Likely Quarternary Molecular Structure file(s) for 1TV9
  • Structure Factors (522 Kb)
  • Retrieve 1TV9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1TV9 from S2C, [Save to disk]
  • Re-refined 1tv9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1TV9 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 1TV9
  • 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 1TV9, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1tv9a3, region A:149-335 [Jmol] [rasmolscript] [script source]
        - Domain d1tv9a1, region A:5-91 [Jmol] [rasmolscript] [script source]
        - Domain d1tv9a2, region A:92-148 [Jmol] [rasmolscript] [script source]
  • Fold representative 1tv9 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1tv9] [1tv9_P] [1tv9_A] [1tv9_D] [1tv9_T]
  • SWISS-PROT database: [P06746]
  • Domain organization of [DPOLB_HUMAN] by SWISSPFAM
  • Domains found in 1TV9: [HhH1] [POLXc ] by SMART
  • Other resources with information on 1TV9
  • Community annotation for 1TV9 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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