3PTA

Crystal structure of human DNMT1(646-1600) in complex with DNA

Structural Biology Knowledgebase: 3PTA SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.291
  • R-Value Work: 0.257

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3PTA

Classification: Transferase / DNA

Total Structure Weight: 120361.53


Macromolecule Entities
Molecule Chains Length Organism Details
DNA (cytosine-5)-methyltransferase 1 A 956 Homo sapiens EC#: 2.1.1.37 IUBMB
Fragment: UNP residues 646-1600
Gene Name(s): DNMT1 Gene View AIM CXXC9 DNMT
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*TP*CP*CP*CP*GP*TP*GP*AP*GP*CP*CP*TP*CP*CP*GP*CP*AP*GP*G)-3') B 19 synthetic
DNA (5'-D(*CP*CP*TP*GP*CP*GP*GP*AP*GP*GP*CP*TP*CP*AP*CP*GP*GP*GP*A)-3') C 19 synthetic

Small Molecules
Ligands 2 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)
ZN
Query on ZN

A 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 (100) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.291
  • R-Value Work: 0.257
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 162.80 α = 90.00
b = 87.90 β = 97.20
c = 113.90 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-12-02
  • Released Date: 2010-12-29
  • Deposition author(s): Song, J., Patel, D.J.

Revision History

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