4DA4

Structure of mouse DNMT1 (731-1602) bound to hemimethylated CpG DNA

Structural Biology Knowledgebase: 4DA4 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.246
  • R-Value Work: 0.196

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4DA4

Classification: Transferase / DNA

Total Structure Weight: 213998.84


Macromolecule Entities
Molecule Chains Length Organism Details
DNA (cytosine-5)-methyltransferase 1 A, B 873 Mus musculus EC#: 2.1.1.37 IUBMB
Fragment: UNP residues 731-1602
Gene Name(s): Dnmt1 Dnmt Met1 Uim
Macromolecule Entities
Molecule Chains Length Organism Details
DNA_UPPER_STRAND C, E 12 synthetic
DNA_LOWER_STRAND D, F 12 synthetic

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

A, B S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CIT
Query on CIT

B CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
SAH IC50: 800 - 4000 nM (85) BindingDB

N/A in BindingMoad
N/A in PDBbind
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
5CM
Query on 5CM
C, E DNA LINKING C10 H16 N3 O7 P DC
C49
Query on C49
D, F DNA LINKING C10 H15 F N3 O7 P S DC

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.246
  • R-Value Work: 0.196
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 89.68 α = 90.00
b = 152.04 β = 94.54
c = 96.05 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-01-12
  • Released Date: 2012-02-22
  • Deposition author(s): Song, J., Patel, D.J.

Revision History

No revisions since initial release