1SKM

HhaI methyltransferase in complex with DNA containing an abasic south carbocyclic sugar at its target site

Structural Biology Knowledgebase: 1SKM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.221
  • R-Value Work: 0.183

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1SKM

Classification: TRANSFERASE / DNA

Total Structure Weight: 45247.14


Macromolecule Entities
Molecule Chains Length Organism Details
Modification methylase HhaI A 327 Haemophilus haemolyticus EC#: 2.1.1.37 IUBMB
Gene Name(s): hhaIM
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*TP*CP*CP*AP*TP*GP*CP*GP*CP*TP*GP*AP*C)-3' C 13 synthetic
5'-D(*T*GP*TP*CP*AP*GP*(HCX)P*GP*CP*AP*TP*GP*G)-3' D 13 synthetic

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SAH
Query on SAH

A S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
HCX
Query on HCX
D NON-POLYMER C7 H13 O4 P --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.221
  • R-Value Work: 0.183
  • Space Group: H 3 2

Unit Cell:

Length (Å) Angle (°)
a = 95.68 α = 90.00
b = 95.68 β = 90.00
c = 315.68 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-03-05
  • Released Date: 2004-08-24
  • Deposition author(s): Horton, J.R., Ratner, G., Banavali, N., Huang, N., Marquez, V.E., MacKerell, A.D., Cheng, X.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4