9ICM Transferase Dna date Dec 16, 1995
title Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With Six Base Pairs Of Double Stranded Dna (No 5'-Phosphate)
authors H.Pelletier, M.R.Sawaya
compound source
Molecule: Dna (5'-D(Cpaptpcptpgpt)-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
178.698 57.867 48.556 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.90 Å
ligand NA enzyme Transferase E.C.2.7.7.7 BRENDA
related structures by homologous chain: 7ICH, 7ICQ
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] (71 Kb) [Save to disk]
  • Biological Unit Coordinates (9icm.pdb1.gz) 63 Kb
  • LPC: Ligand-Protein Contacts for 9ICM
  • CSU: Contacts of Structural Units for 9ICM
  • Likely Quarternary Molecular Structure file(s) for 9ICM
  • Structure Factors (99 Kb)
  • Retrieve 9ICM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 9ICM from S2C, [Save to disk]
  • Re-refined 9icm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 9ICM 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 9ICM
  • 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 9ICM, from MSDmotif at EBI
  • Genome occurence of 9ICM's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d9icma4, region A:149-335 [Jmol] [rasmolscript] [script source]
        - Domain d9icma1, region A:9-91 [Jmol] [rasmolscript] [script source]
        - Domain d9icma3, region A:92-148 [Jmol] [rasmolscript] [script source]
  • Fold representative 9icm 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: [9icm_P] [9icm] [9icm_T] [9icm_A]
  • SWISS-PROT database: [P06746]
  • Domain organization of [DPOLB_HUMAN] by SWISSPFAM
  • Domains found in 9ICM: [HhH1] [POLXc ] by SMART
  • Other resources with information on 9ICM
  • Community annotation for 9ICM 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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