3BDP Transferase Dna date Nov 17, 1997
title Dna Polymerase Idna Complex
authors J.R.Kiefer, C.Mao, L.S.Beese
compound source
Molecule: Dna (5'-D(Gpcpaptpgpaptpgpcp2dt)-3')
Chain: P
Engineered: Yes
Synthetic: Yes

Molecule: Dna (5'-D(Apgpcpaptpcpaptpgpc)-3')
Chain: T
Engineered: Yes

Synthetic: Yes

Molecule: Protein (Dna Polymerase I)
Chain: A
Fragment: Residues 297-876
Synonym: Bf
Ec: 2.7.7.7
Engineered: Yes

Organism_scientific: Geobacillus Stearothermophilus
Organism_taxid: 1422
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.250 R_Free 0.294
crystal
cell
length a length b length c angle alpha angle beta angle gamma
87.063 93.547 106.252 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand 2DT, SO4 enzyme Transferase E.C.2.7.7.7 BRENDA
related structures by homologous chain: 1L5U, 1XC9
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceVisualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal., Kiefer JR, Mao C, Braman JC, Beese LS, Nature 1998 Jan 15;391(6664):304-7. PMID:9440698
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (115 Kb) [Save to disk]
  • Biological Unit Coordinates (3bdp.pdb1.gz) 111 Kb
  • LPC: Ligand-Protein Contacts for 3BDP
  • CSU: Contacts of Structural Units for 3BDP
  • Likely Quarternary Molecular Structure file(s) for 3BDP
  • Structure Factors (554 Kb)
  • Retrieve 3BDP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3BDP from S2C, [Save to disk]
  • Re-refined 3bdp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3BDP 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 3BDP
  • 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 3BDP, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d3bdpa1, region A:297-468 [Jmol] [rasmolscript] [script source]
        - Domain d3bdpa2, region A:469-876 [Jmol] [rasmolscript] [script source]
  • Fold representative 3bdp 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: [3bdp_P] [3bdp_A] [3bdp_T] [3bdp]
  • SWISS-PROT database: [P52026]
  • Domain organization of [DPO1_BACST] by SWISSPFAM
  • Domains found in 3BDP: [35EXOc] [POLAc ] by SMART
  • Other resources with information on 3BDP
  • Community annotation for 3BDP 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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