1N56 Transferase Dna date Nov 04, 2002
title Y-Family Dna Polymerase Dpo4 In Complex With Dna Containing Lesion
authors H.Ling, F.Boudsocq, R.Woodgate, W.Yang
compound source
Molecule: 5'-D(Gpgpgpgpgpapapgpgpapcptpapa)-3
Chain: C, E
Engineered: Yes
Other_details: Template
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: 5'-D(Tpcpaptp(3dr) Papgptpcpcptptpcpcpcpcpc)-3';
Chain: D, F
Engineered: Yes
Other_details: Primer

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna Polymerase Iv
Chain: A, B
Synonym: Dpo4, Pol Iv, Repair Dna Polymerase Of The Dinbum Superfamily, Dinp;
Engineered: Yes

Organism_scientific: Sulfolobus Solfataricus
Organism_taxid: 2287
Gene: Dpo4
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22bb
symmetry Space Group: P 21 21 21
R_factor 0.225 R_Free 0.263
crystal
cell
length a length b length c angle alpha angle beta angle gamma
98.016 102.358 105.660 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand 3DR, ATP, CA, MG enzyme
related structures by homologous chain: 1S0M, 1S97
Gene
Ontology
ChainFunctionProcessComponent
A, B


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (151 Kb) [Save to disk]
  • Biological Unit Coordinates (1n56.pdb1.gz) 74 Kb
  • Biological Unit Coordinates (1n56.pdb2.gz) 74 Kb
  • LPC: Ligand-Protein Contacts for 1N56
  • CSU: Contacts of Structural Units for 1N56
  • Likely Quarternary Molecular Structure file(s) for 1N56
  • Structure Factors (388 Kb)
  • Retrieve 1N56 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1N56 from S2C, [Save to disk]
  • Re-refined 1n56 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1N56 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 1N56
  • 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 1N56, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1n56a2, region A:1-240 [Jmol] [rasmolscript] [script source]
        - Domain d1n56a1, region A:241-341 [Jmol] [rasmolscript] [script source]
        - Domain d1n56b2, region B:1-240 [Jmol] [rasmolscript] [script source]
        - Domain d1n56b1, region B:241-341 [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: [1n56_C] [1n56_E] [1n56] [1n56_B] [1n56_D] [1n56_A] [1n56_F]
  • SWISS-PROT database: [Q97W02]
  • Domain organization of [DPO42_SULSO] by SWISSPFAM
  • Other resources with information on 1N56
  • Community annotation for 1N56 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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