1SKM Transferase Dna date Mar 05, 2004
title Hhai Methyltransferase In Complex With Dna Containing An Aba Carbocyclic Sugar At Its Target Site
authors J.R.Horton, G.Ratner, N.Banavali, N.Huang, V.E.Marquez, A.D.Macke X.Cheng
compound source
Molecule: 5'-D(Tpcpcpaptpgpcpgpcptpgpapc)-3'
Chain: C
Engineered: Yes
Synthetic: Yes

Molecule: 5'-D(Tgptpcpapgp(Hcx)Pgpcpaptpgpg)-3
Chain: D
Engineered: Yes

Synthetic: Yes

Molecule: Modification Methylase Hhai
Chain: A
Synonym: Cytosine-Specific Methyltransferase Hhai, M.Hhai
Ec: 2.1.1.37
Engineered: Yes

Organism_scientific: Haemophilus Haemolyticus
Organism_taxid: 726
Gene: Hhaim
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: H 3 2
R_factor 0.183 R_Free 0.221
crystal
cell
length a length b length c angle alpha angle beta angle gamma
95.681 95.681 315.683 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.20 Å
ligand HCX, SAH enzyme Transferase E.C.2.1.1.37 BRENDA
related structures by homologous chain: 1FJX, 6MHT
Gene
Ontology
ChainFunctionProcessComponent
A
  • DNA (cytosine-5-)-methyltran...


  • Primary referenceCaught in the act: visualization of an intermediate in the DNA base-flipping pathway induced by HhaI methyltransferase., Horton JR, Ratner G, Banavali NK, Huang N, Choi Y, Maier MA, Marquez VE, MacKerell AD Jr, Cheng X, Nucleic Acids Res 2004 Jul 23;32(13):3877-86. Print 2004. PMID:15273274
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (73 Kb) [Save to disk]
  • Biological Unit Coordinates (1skm.pdb1.gz) 68 Kb
  • LPC: Ligand-Protein Contacts for 1SKM
  • CSU: Contacts of Structural Units for 1SKM
  • Likely Quarternary Molecular Structure file(s) for 1SKM
  • Retrieve 1SKM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1SKM from S2C, [Save to disk]
  • View 1SKM 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 1SKM
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1SKM, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1skma_, 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: [1skm_C] [1skm_A] [1skm_D] [1skm]
  • SWISS-PROT database: [P05102]
  • Domain organization of [MTH1_HAEPH] by SWISSPFAM
  • Other resources with information on 1SKM
  • Community annotation for 1SKM 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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