2DPM Transferase date Sep 03, 1998
title Dpnm Dna Adenine Methyltransferase From Streptoccocus Pneumo Complexed With S-Adenosylmethionine
authors P.H.Tran, Z.R.Korszun, S.Cerritelli, S.S.Springhorn, S.A.Lacks
compound source
Molecule: Protein (Adenine-Specific Methyltransferase Dpnii
Chain: A
Synonym: M.Dpnii 1
Ec: 2.1.1.72
Engineered: Yes
Other_details: S-Adenosylmethionine
Organism_scientific: Streptococcus Pneumoniae
Organism_taxid: 1313
Strain: Hb264
Gene: Dpnm
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_plasmid: Pls211
Expression_system_gene: Dpnm
symmetry Space Group: P 21 21 21
R_factor 0.238 R_Free 0.284
crystal
cell
length a length b length c angle alpha angle beta angle gamma
56.600 68.100 85.200 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand HG, SAM enzyme Transferase E.C.2.1.1.72 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal structure of the DpnM DNA adenine methyltransferase from the DpnII restriction system of streptococcus pneumoniae bound to S-adenosylmethionine., Tran PH, Korszun ZR, Cerritelli S, Springhorn SS, Lacks SA, Structure. 1998 Dec 15;6(12):1563-75. PMID:9862809
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (51 Kb) [Save to disk]
  • Biological Unit Coordinates (2dpm.pdb1.gz) 47 Kb
  • LPC: Ligand-Protein Contacts for 2DPM
  • CSU: Contacts of Structural Units for 2DPM
  • Likely Quarternary Molecular Structure file(s) for 2DPM
  • Retrieve 2DPM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2DPM from S2C, [Save to disk]
  • View 2DPM 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 2DPM
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2DPM, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d2dpma_, region A [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: [2dpm] [2dpm_A]
  • SWISS-PROT database: [P04043]
  • Domain organization of [MTD21_STRPN] by SWISSPFAM
  • Other resources with information on 2DPM
  • Community annotation for 2DPM 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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