1BPZ Transferase Dna date Feb 03, 2004
title Human Dna Polymerase Beta Complexed With Nicked Dna
authors M.R.Sawaya, R.Prasad, S.H.Wilson, J.Kraut, H.Pelletier
compound source
Molecule: Dna (5'-D(Cpcpgpapcpcpapcpgpcpaptpcp 3');
Chain: T
Engineered: Yes
Synthetic: Yes

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

Synthetic: Yes

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

Synthetic: Yes

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
R_Free NULL
crystal
cell
length a length b length c angle alpha angle beta angle gamma
53.535 78.656 54.618 90.00 107.54 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: 1HUO, 1ZQA
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] (73 Kb) [Save to disk]
  • Biological Unit Coordinates (1bpz.pdb1.gz) 67 Kb
  • LPC: Ligand-Protein Contacts for 1BPZ
  • CSU: Contacts of Structural Units for 1BPZ
  • Likely Quarternary Molecular Structure file(s) for 1BPZ
  • Structure Factors (105 Kb)
  • Retrieve 1BPZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1BPZ from S2C, [Save to disk]
  • Re-refined 1bpz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1BPZ 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 1BPZ
  • 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
  • 3D motif for 1BPZ, from MSDmotif at EBI
  • Genome occurence of 1BPZ's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1bpza4, region A:149-335 [Jmol] [rasmolscript] [script source]
        - Domain d1bpza1, region A:5-91 [Jmol] [rasmolscript] [script source]
        - Domain d1bpza3, region A:92-148 [Jmol] [rasmolscript] [script source]
  • 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: [1bpz_D] [1bpz] [1bpz_P] [1bpz_T] [1bpz_A]
  • SWISS-PROT database: [P06746]
  • Domain organization of [DPOLB_HUMAN] by SWISSPFAM
  • Domains found in 1BPZ: [HhH1] [POLXc ] by SMART
  • Other resources with information on 1BPZ
  • Community annotation for 1BPZ 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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