1N3C Hydrolase, Lyase Dna date Oct 25, 2002
title Structural And Biochemical Exploration Of A Critical Amino Acid In Human 8-Oxoguanine Glycosylase
authors D.P.Norman, S.J.Chung, G.L.Verdine
compound source
Molecule: Dna Complement Strand
Chain: B
Engineered: Yes
Synthetic: Yes

Molecule: 8-Oxog-Containing Dna
Chain: C
Engineered: Yes

Synthetic: Yes

Molecule: N-Glycosylasedna Lyase
Chain: A
Fragment: 3.2.2.-, 4.2.99.18
Synonym: Hogg1 Glycosylase, 8-Oxoguanosine Dna Glycosylasedna-(Apurinic Or Apyrimidinic Site) Lyase;
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ogg1
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet30a
symmetry Space Group: P 65 2 2
R_factor 0.225 R_Free 0.273
crystal
cell
length a length b length c angle alpha angle beta angle gamma
92.255 92.255 210.600 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.70 Å
ligand 8OG, CA enzyme
related structures by homologous chain: 1FN7
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase., Norman DP, Chung SJ, Verdine GL, Biochemistry 2003 Feb 18;42(6):1564-72. PMID:12578369
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (70 Kb) [Save to disk]
  • Biological Unit Coordinates (1n3c.pdb1.gz) 65 Kb
  • LPC: Ligand-Protein Contacts for 1N3C
  • CSU: Contacts of Structural Units for 1N3C
  • Likely Quarternary Molecular Structure file(s) for 1N3C
  • Retrieve 1N3C in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1N3C from S2C, [Save to disk]
  • View 1N3C 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 1N3C
  • 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 1N3C, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1n3ca1, region A:136-325 [Jmol] [rasmolscript] [script source]
        - Domain d1n3ca2, region A:9-135 [Jmol] [rasmolscript] [script source]
  • Fold representative 1n3c 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: [1n3c_C] [1n3c_A] [1n3c] [1n3c_B]
  • SWISS-PROT database: [O15527]
  • Domain organization of [OGG1_HUMAN] by SWISSPFAM
  • Domain found in 1N3C: [ENDO3c ] by SMART
  • Other resources with information on 1N3C
  • Community annotation for 1N3C 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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