1K82 Hydrolase Dna date Oct 22, 2001
title Crystal Structure Of E.Coli Formamidopyrimidine-Dna Glycosylase (Fpg) Covalently Trapped With Dna
authors R.Gilboa, D.O.Zharkov, G.Golan, A.S.Fernandes, S.E.Gerchman, E.Matz, J.H.Kycia, A.P.Grollman, G.Shoham
compound source
Molecule: 5'-D(Gpgpcptptpcpcptpcpcptpgpg)-3'
Chain: E, F, G, H
Synonym: Fapy-Dna Glycosylase, Fpg
Engineered: Yes
Synthetic: Yes

Molecule: 5'-D(Cpcpapgpgpap(Ped)Pgpapapgpcpc)- 3';
Chain: I, J, K, L
Engineered: Yes

Synthetic: Yes

Molecule: Formamidopyrimidine-Dna Glycosylase
Chain: A, B, C, D
Ec: 3.2.2.23
Engineered: Yes

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Fpg
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: B834(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-13a
symmetry Space Group: P 1 21 1
R_factor 0.214 R_Free 0.265
crystal
cell
length a length b length c angle alpha angle beta angle gamma
80.704 96.033 96.228 90.00 96.80 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand PED, ZN enzyme Hydrolase E.C.3.2.2.23 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B
  • endonuclease activity


  • Primary referenceStructure of formamidopyrimidine-DNA glycosylase covalently complexed to DNA., Gilboa R, Zharkov DO, Golan G, Fernandes AS, Gerchman SE, Matz E, Kycia JH, Grollman AP, Shoham G, J Biol Chem 2002 May 31;277(22):19811-6. PMID:11912217
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (221 Kb) [Save to disk]
  • Biological Unit Coordinates (1k82.pdb1.gz) 57 Kb
  • Biological Unit Coordinates (1k82.pdb2.gz) 56 Kb
  • Biological Unit Coordinates (1k82.pdb3.gz) 56 Kb
  • Biological Unit Coordinates (1k82.pdb4.gz) 56 Kb
  • LPC: Ligand-Protein Contacts for 1K82
  • CSU: Contacts of Structural Units for 1K82
  • Likely Quarternary Molecular Structure file(s) for 1K82
  • Retrieve 1K82 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1K82 from S2C, [Save to disk]
  • View 1K82 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 1K82
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1K82, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1k82a2, region A:1-128 [Jmol] [rasmolscript] [script source]
        - Domain d1k82a1, region A:129-216 [Jmol] [rasmolscript] [script source]
        - Domain d1k82a3, region A:225-268 [Jmol] [rasmolscript] [script source]
        - Domain d1k82b2, region B:1-128 [Jmol] [rasmolscript] [script source]
        - Domain d1k82b1, region B:129-216 [Jmol] [rasmolscript] [script source]
        - Domain d1k82b3, region B:225-268 [Jmol] [rasmolscript] [script source]
        - Domain d1k82c2, region C:1-128 [Jmol] [rasmolscript] [script source]
        - Domain d1k82c1, region C:129-216 [Jmol] [rasmolscript] [script source]
        - Domain d1k82c3, region C:225-268 [Jmol] [rasmolscript] [script source]
        - Domain d1k82d2, region D:1-128 [Jmol] [rasmolscript] [script source]
        - Domain d1k82d1, region D:129-216 [Jmol] [rasmolscript] [script source]
        - Domain d1k82d3, region D:225-268 [Jmol] [rasmolscript] [script source]
  • Fold representative 1k82 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: [1k82_E] [1k82_C] [1k82_J] [1k82_G] [1k82_I] [1k82_H] [1k82_F] [1k82_L] [1k82_D] [1k82] [1k82_A] [1k82_B] [1k82_K]
  • SWISS-PROT database: [P05523]
  • Domain organization of [FPG_ECOLI] by SWISSPFAM
  • Domains found in 1K82: [Fapy_DNA_glyco] [H2TH ] by SMART
  • Other resources with information on 1K82
  • Community annotation for 1K82 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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