1K3W Hydrolase Dna date Oct 04, 2001
title Crystal Structure Of A Trapped Reaction Intermediate Of The Enzyme Endonuclease Viii With Dna
authors G.Golan, D.O.Zharkov, R.Gilboa, A.S.Fernandes, J.H.Kycia, S.E.Ger R.A.Rieger, A.P.Grollman, G.Shoham
compound source
Molecule: 5'-D(Gpgpcptptpcpaptpcpcptpgpg)-3'
Chain: B
Engineered: Yes
Synthetic: Yes

Molecule: 5'-D(Cpcpapgpgpap(Ped)Pgpapapgpcpc)-
Chain: C
Engineered: Yes

Synthetic: Yes

Molecule: Endonuclease Viii
Chain: A
Ec: 3.2.2.-
Engineered: Yes

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Nei
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: B834(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet13a
symmetry Space Group: P 43 2 2
length a length b length c angle alpha angle beta angle gamma
76.030 76.030 164.933 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.42 Å
ligand PED, SO4, ZN enzyme Hydrolase E.C.3.2.2 BRENDA
related structures by homologous chain: 1K3X, 1Q3B
  • endonuclease activity

  • Primary referenceStructural analysis of an Escherichia coli endonuclease VIII covalent reaction intermediate., Zharkov DO, Golan G, Gilboa R, Fernandes AS, Gerchman SE, Kycia JH, Rieger RA, Grollman AP, Shoham G, EMBO J 2002 Feb 15;21(4):789-800. PMID:11847126
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (122 Kb) [Save to disk]
  • Biological Unit Coordinates (1k3w.pdb1.gz) 117 Kb
  • LPC: Ligand-Protein Contacts for 1K3W
  • CSU: Contacts of Structural Units for 1K3W
  • Likely Quarternary Molecular Structure file(s) for 1K3W
  • Retrieve 1K3W in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1K3W from S2C, [Save to disk]
  • View 1K3W 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 1K3W
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Conformational Epitope Prediction for 1K3W 1K3WA 1K3WB 1K3WC from the CEP Server.
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1K3W, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1k3wa2, region A:1-124 [Jmol] [rasmolscript] [script source]
        - Domain d1k3wa1, region A:125-214 [Jmol] [rasmolscript] [script source]
        - Domain d1k3wa3, region A:223-262 [Jmol] [rasmolscript] [script source]
  • Fold representative 1k3w 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: [1k3w_C] [1k3w_B] [1k3w] [1k3w_A]
  • SWISS-PROT database: [P50465]
  • Domain organization of [END8_ECOLI] by SWISSPFAM
  • Domains found in 1K3W: [Fapy_DNA_glyco] [H2TH ] by SMART
  • Other resources with information on 1K3W
  • Community annotation for 1K3W 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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