3EPZ

Structure of the replication foci-targeting sequence of human DNA cytosine methyltransferase DNMT1

• PDB DOI: https://doi.org/10.2210/pdb3EPZ/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-09-30 Released: 2008-11-25 
• Deposition Author(s): Walker, J.R., Avvakumov, G.V., Xue, S., Li, Y., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free: 0.264 
• R-Value Work: 0.213 
• R-Value Observed: 0.216 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 61.26 kDa 
• Atom Count: 3,560 
• Modelled Residue Count: 450 
• Deposited Residue Count: 536 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA (cytosine-5)-methyltransferase 1	A, B	268	Homo sapiens	Mutation(s): 0  Gene Names: AIM, CXX9, CXXC9, DNMT, DNMT1 EC: 2.1.1.37
UniProt & NIH Common Fund Data Resources
Find proteins for P26358 (Homo sapiens) Explore P26358  Go to UniProtKB:  P26358
PHAROS:  P26358 GTEx:  ENSG00000130816

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BGC	D [auth A]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	C [auth A], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA	F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free: 0.264 
• R-Value Work: 0.213 
• R-Value Observed: 0.216 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.544	α = 90
b = 59.768	β = 92.31
c = 96.286	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-11-25 
Deposition Author(s): Walker, J.R., Avvakumov, G.V., Xue, S., Li, Y., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2008-11-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2011-09-14
  Changes: Database references
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary