3BO5 | pdb_00003bo5

Crystal structure of methyltransferase domain of human Histone-lysine N-methyltransferase SETMAR

• PDB DOI: https://doi.org/10.2210/pdb3BO5/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-12-17 Released: 2008-01-22 
• Deposition Author(s): Lunin, V.V., Wu, H., Ren, H., Dobrovetsky, E., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Min, J., Plotnikov, A.N., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 
  0.199 (Depositor), 0.197 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.152 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Literature

The Crystal Structure of Methyltransferase Domain of Human Histone-lysine N-methyltransferase SETMAR in Complex With AdoHcy.

Wu, H., Lunin, V.V., Ren, H., Dobrovetsky, E., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Min, J., Plotnikov, A.N.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 33.13 kDa 
• Atom Count: 2,467 
• Modeled Residue Count: 269 
• Deposited Residue Count: 290 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase SETMAR	A	290	Homo sapiens	Mutation(s): 2  Gene Names: SETMAR EC: 2.1.1.43 (PDB Primary Data), 3.1 (UniProt), 2.1.1.357 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q53H47 (Homo sapiens) Explore Q53H47  Go to UniProtKB:  Q53H47
PHAROS:  Q53H47 GTEx:  ENSG00000170364

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	F [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
GOL	G [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A], C [auth A], D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free:  0.199 (Depositor), 0.197 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.152 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.396	α = 90
b = 67.827	β = 105.93
c = 44.637	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-01-22 
Deposition Author(s): Lunin, V.V., Wu, H., Ren, H., Dobrovetsky, E., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Min, J., Plotnikov, A.N., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2008-01-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.3: 2024-02-21
  Changes: Data collection