9ICX Transferase Dna date Oct 24, 1996
title Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With Six Base Pairs Of Dna (Non Gapped Dna Only)
authors H.Pelletier, M.R.Sawaya
compound source
Molecule: Dna (5'-D(Cpaptpcptpg)-3')
Chain: T
Engineered: Yes
Synthetic: Yes

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

Synthetic: Yes

Molecule: Protein (Dna Polymerase Beta (E.C.2.7.7.7))
Chain: A
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 2
R_factor
R_Free NULL
crystal
cell
length a length b length c angle alpha angle beta angle gamma
179.010 57.729 48.511 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.60 Å
ligand NA enzyme Transferase E.C.2.7.7.7 BRENDA
related structures by homologous chain: 1ZQU, 9ICW
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal structures of human DNA polymerase beta complexed with DNA: implications for catalytic mechanism, processivity, and fidelity., Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J, Biochemistry. 1996 Oct 1;35(39):12742-61. PMID:8841118
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (69 Kb) [Save to disk]
  • Biological Unit Coordinates (9icx.pdb1.gz) 62 Kb
  • LPC: Ligand-Protein Contacts for 9ICX
  • CSU: Contacts of Structural Units for 9ICX
  • Likely Quarternary Molecular Structure file(s) for 9ICX
  • Structure Factors (102 Kb)
  • Retrieve 9ICX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 9ICX from S2C, [Save to disk]
  • Re-refined 9icx structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 9ICX 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 9ICX
  • 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 9ICX, from MSDmotif at EBI
  • Genome occurence of 9ICX's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d9icxa4, region A:149-335 [Jmol] [rasmolscript] [script source]
        - Domain d9icxa1, region A:9-91 [Jmol] [rasmolscript] [script source]
        - Domain d9icxa3, region A:92-148 [Jmol] [rasmolscript] [script source]
  • Fold representative 9icx 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: [9icx_P] [9icx_T] [9icx_A] [9icx]
  • SWISS-PROT database: [P06746]
  • Domain organization of [DPOLB_HUMAN] by SWISSPFAM
  • Domains found in 9ICX: [HhH1] [POLXc ] by SMART
  • Other resources with information on 9ICX
  • Community annotation for 9ICX 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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