1VAS Hydrolase Dna date Sep 08, 1995
title Atomic Model Of A Pyrimidine Dimer Specific Excision Repair Complexed With A Dna Substrate: Structural Basis For Damage Recognition
authors D.G.Vassylyev, T.Kashiwagi, Y.Mikami, M.Ariyoshi, S.Iwai, E.Ohtsu K.Morikawa
compound source
Molecule: Dna (5'-D(Aptpcpgpcpgptptpgpcpgpcpt)
Chain: B
Engineered: Yes
 Synthetic: Yes

Molecule: Dna (5'-D(Tpapgpcpgpcpapapcpgpcpgpa)
Chain: C
Engineered: Yes
Synthetic: Yes

Molecule: Protein (T4 Endonuclease V (E.C.3.1.25.1))
Chain: A
Engineered: Yes
Organism_scientific: Enterobacteria Phage T4
Organism_taxid: 10665
Gene: Denv
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_gene: Denv
symmetry Space Group: P 65
R_factor 0.152 R_Free 0.240
crystal
cell
length a length b length c angle alpha angle beta angle gamma
118.820 118.820 36.280 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.75 Å
ligand
enzyme Hydrolase E.C.3.1.25.1 BRENDA
note 1VAS (Molecule of the Month:pdb91)
related structures by homologous chain: 1ENI
Gene
Ontology
ChainFunctionProcessComponent
A
  • nuclease activity
  • endonuclease activity


    • Primary referenceAtomic model of a pyrimidine dimer excision repair enzyme complexed with a DNA substrate: structural basis for damaged DNA recognition., Vassylyev DG, Kashiwagi T, Mikami Y, Ariyoshi M, Iwai S, Ohtsuka E, Morikawa K, Cell 1995 Dec 1;83(5):773-82. PMID:8521494
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (40 Kb) [Save to disk]
  • Biological Unit Coordinates (1vas.pdb1.gz) 36 Kb
  • CSU: Contacts of Structural Units for 1VAS
  • Likely Quarternary Molecular Structure file(s) for 1VAS
  • Structure Factors (29 Kb)
  • Retrieve 1VAS in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1VAS from S2C, [Save to disk]
  • Re-refined 1vas structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1VAS 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 1VAS
  • 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 1VAS, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1vasa_, region A [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: [1vas_A] [1vas] [1vas_B] [1vas_C]
  • SWISS-PROT database: [P04418]
  • Domain organization of [END5_BPT4] by SWISSPFAM
    • Other resources with information on 1VAS
  • Community annotation for 1VAS 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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