1YFJ

T4Dam in Complex with AdoHcy and 15-mer Oligonucleotide Showing Semi-specific and Specific Contact


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.202

Literature

Macromolecules
Sequence Display for 1YFJ

Classification: TRANSFERASE / DNA

Total Structure Weight: 231149.67


Macromolecule Entities
Molecule Chains Length Organism Details
DNA adenine methylase A, B, C..., D, E, FA, B, C, D, E, F 259 Escherichia virus t4 EC#: 2.1.1.72 IUBMB
Mutation: Q139R, Y140F, Q209L
Gene Name(s): DAM
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*TP*CP*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*TP*G)-3' 0, 1, 2... , 3, 4, 5, 6, 7, 8, 9 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 15 synthetic

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

A, B, C, D, E, F S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

2, 4 CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

1, 2, 8 CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.202
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 111.20 α = 90.00
b = 133.00 β = 90.00
c = 189.20 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-01-02
  • Released Date: 2005-05-17
  • Deposition author(s): Horton, J.R., Liebert, K., Hattman, S., Jeltsch, A., Cheng, X.

Revision History

  • Version 1_0: 2005-05-17

    Type: Initial release

  • Version 1_1: 2008-04-30

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Version format compliance

  • Version 1_3: 2017-10-11

    Type: Refinement description