2FMS Transferase Dna date Jan 09, 2006
title Dna Polymerase Beta With A Gapped Dna Substrate And Dumpnpp With Magnesium In The Catalytic Site
authors V.K.Batra, W.A.Beard, D.D.Shock, J.M.Krahn, L.C.Pedersen, S.H.Wilson
compound source
Molecule: 5'- D(Cpcpgpapcpapgpcpgpcpaptpcpapgpc)-3';
Chain: T
Engineered: Yes
Synthetic: Yes

Molecule: 5'-D(Gpcptpgpaptpgpcpgpc)-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, 4.2.99.-
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 0.196 R_Free 0.244
crystal
cell
length a length b length c angle alpha angle beta angle gamma
50.800 80.400 55.500 90.00 107.90 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand CL, DUP, MG, NA enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceMagnesium-induced assembly of a complete DNA polymerase catalytic complex., Batra VK, Beard WA, Shock DD, Krahn JM, Pedersen LC, Wilson SH, Structure. 2006 Apr;14(4):757-66. PMID:16615916
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (80 Kb) [Save to disk]
  • Biological Unit Coordinates (2fms.pdb1.gz) 75 Kb
  • LPC: Ligand-Protein Contacts for 2FMS
  • CSU: Contacts of Structural Units for 2FMS
  • Likely Quarternary Molecular Structure file(s) for 2FMS
  • Structure Factors (230 Kb)
  • Retrieve 2FMS in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2FMS from S2C, [Save to disk]
  • Re-refined 2fms structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2FMS 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 2FMS
  • 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 2FMS, from MSDmotif at EBI
  • Fold representative 2fms from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2fms] [2fms_A] [2fms_T] [2fms_D] [2fms_P]
  • SWISS-PROT database: [P06746]
  • Domain organization of [DPOLB_HUMAN] by SWISSPFAM
  • Domains found in 2FMS: [HhH1] [POLXc ] by SMART
  • Other resources with information on 2FMS
  • Community annotation for 2FMS 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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