1BPY Transferase Dna date Apr 15, 1997
title Human Dna Polymerase Beta Complexed With Gapped Dna And Ddct
authors M.R.Sawaya, H.Pelletier, R.Prasad, S.H.Wilson, J.Kraut
compound source
Molecule: Dna (5'-D(Cpcpgpapcpgpgpcpgpcpaptpcp 3');
Chain: T
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

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

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

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

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Protein (Dna Polymerase Beta)
Chain: A
Synonym: Pol Beta, Beta-Pol
Ec: 2.7.7.7
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cellular_location: Nucleus
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.232 R_Free 0.330
crystal
cell
length a length b length c angle alpha angle beta angle gamma
50.543 79.817 54.942 90.00 107.11 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand DCT, DOC, MG, NA enzyme Transferase E.C.2.7.7.7 BRENDA
related structures by homologous chain: 1BPB, 1TV9
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism., Sawaya MR, Prasad R, Wilson SH, Kraut J, Pelletier H, Biochemistry 1997 Sep 16;36(37):11205-15. PMID:9287163
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (81 Kb) [Save to disk]
  • Biological Unit Coordinates (1bpy.pdb1.gz) 75 Kb
  • LPC: Ligand-Protein Contacts for 1BPY
  • CSU: Contacts of Structural Units for 1BPY
  • Likely Quarternary Molecular Structure file(s) for 1BPY
  • Structure Factors (146 Kb)
  • Retrieve 1BPY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1BPY from S2C, [Save to disk]
  • Re-refined 1bpy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1BPY 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 1BPY
  • 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 1BPY, from MSDmotif at EBI
  • Genome occurence of 1BPY's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1bpya1, region A:10-91 [Jmol] [rasmolscript] [script source]
        - Domain d1bpya4, region A:149-335 [Jmol] [rasmolscript] [script source]
        - Domain d1bpya3, region A:92-148 [Jmol] [rasmolscript] [script source]
  • Fold representative 1bpy 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: [1bpy_A] [1bpy] [1bpy_P] [1bpy_D] [1bpy_T]
  • SWISS-PROT database: [P06746]
  • Domain organization of [DPOLB_HUMAN] by SWISSPFAM
  • Domains found in 1BPY: [HhH1] [POLXc ] by SMART
  • Other resources with information on 1BPY
  • Community annotation for 1BPY 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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