1M3Q Hydrolase Dna date Jun 28, 2002
title Crystal Structure Of Hogg1 D268e Mutant With Base-Excised Dn Aminoguanine
authors S.J.Chung, G.L.Verdine
compound source
Molecule: 5'-D(Gpgptpapgpapcpcptpgpgpapcpgpc
Chain: B
Engineered: Yes
Synthetic: Yes

Molecule: 5'-D(Gpcpgptpcpcpap(Drz)Pgptpcptpap
Chain: C
Engineered: Yes

Synthetic: Yes

Molecule: 8-Oxoguanine Dna Glycosylase
Chain: A
Fragment: Core Fragment (Residues 12-325)
Ec: 3.2.2.-
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ogg1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
symmetry Space Group: P 65 2 2
R_factor 0.235 R_Free 0.268
crystal
cell
length a length b length c angle alpha angle beta angle gamma
92.415 92.415 211.425 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.90 Å
ligand ANG, CA, DRZ enzyme Hydrolase E.C.3.2.2 BRENDA
related structures by homologous chain: 1LWY
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructures of end products resulting from lesion processing by a DNA glycosylase/lyase., Chung SJ, Verdine GL, Chem Biol 2004 Dec;11(12):1643-9. PMID:15610848
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (70 Kb) [Save to disk]
  • Biological Unit Coordinates (1m3q.pdb1.gz) 64 Kb
  • LPC: Ligand-Protein Contacts for 1M3Q
  • CSU: Contacts of Structural Units for 1M3Q
  • Likely Quarternary Molecular Structure file(s) for 1M3Q
  • Structure Factors (561 Kb)
  • Retrieve 1M3Q in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1M3Q from S2C, [Save to disk]
  • Re-refined 1m3q structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1M3Q 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 1M3Q
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1M3Q, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1m3qa1, region A:136-325 [Jmol] [rasmolscript] [script source]
        - Domain d1m3qa2, region A:9-135 [Jmol] [rasmolscript] [script source]
  • Fold representative 1m3q 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: [1m3q_C] [1m3q] [1m3q_B] [1m3q_A]
  • SWISS-PROT database: [O15527]
  • Domain organization of [OGG1_HUMAN] by SWISSPFAM
  • Domain found in 1M3Q: [ENDO3c ] by SMART
  • Other resources with information on 1M3Q
  • Community annotation for 1M3Q 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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