4SKN Hydrolase Dna date Feb 20, 1999
title A Nucleotide-Flipping Mechanism From The Structure Of Human Glycosylase Bound To Dna
authors G.Slupphaug, C.D.Mol, B.Kavli, A.S.Arvai, H.E.Krokan, J.A.Tainer
compound source
Molecule: Dna (5'-D(Tpgpgpgp(D1p)Pgpgpcptpt)-3')
Chain: A
Engineered: Yes
Synthetic: Yes

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

Synthetic: Yes

Molecule: Protein (Uracil-Dna Glycosylase)
Chain: E
Synonym: Udg, Ung
Ec: 3.2.2.3
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.189 R_Free 0.273
crystal
cell
length a length b length c angle alpha angle beta angle gamma
48.830 65.660 97.150 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.90 Å
ligand ORP, URA enzyme Hydrolase E.C.3.2.2.3 BRENDA
related structures by homologous chain: 2SSP
Gene
Ontology
ChainFunctionProcessComponent
E


Primary referenceA nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA., Slupphaug G, Mol CD, Kavli B, Arvai AS, Krokan HE, Tainer JA, Nature 1996 Nov 7;384(6604):87-92. PMID:8900285
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (50 Kb) [Save to disk]
  • Biological Unit Coordinates (4skn.pdb1.gz) 46 Kb
  • LPC: Ligand-Protein Contacts for 4SKN
  • CSU: Contacts of Structural Units for 4SKN
  • Likely Quarternary Molecular Structure file(s) for 4SKN
  • Structure Factors (97 Kb)
  • Retrieve 4SKN in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4SKN from S2C, [Save to disk]
  • Re-refined 4skn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4SKN 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 4SKN
  • 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 4SKN, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d4skne_, region E [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: [4skn] [4skn_A] [4skn_B] [4skn_E]
  • SWISS-PROT database: [P13051]
  • Domain organization of [UNG_HUMAN] by SWISSPFAM
  • Domains found in 4SKN: [UDG] [UreE_C ] by SMART
  • Other resources with information on 4SKN
  • Community annotation for 4SKN 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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