3MEK

Crystal Structure of Human Histone-Lysine N-methyltransferase SMYD3 in Complex with S-adenosyl-L-methionine

• PDB DOI: https://doi.org/10.2210/pdb3MEK/pdb

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


• Deposited: 2010-03-31 Released: 2010-04-14 
• Deposition Author(s): Lam, R., Dombrovski, L., Li, Y., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Min, J., Wu, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.208 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 

Literature

Crystal Structure of Human Histone-Lysine N-methyltransferase SMYD3 in Complex with S-adenosyl-L-methionine

Lam, R., Dombrovski, L., Li, Y., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Min, J., Wu, H.

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: 50.58 kDa 
• Atom Count: 3,559 
• Modelled Residue Count: 423 
• Deposited Residue Count: 429 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SET and MYND domain-containing protein 3	A	429	Homo sapiens	Mutation(s): 0  Gene Names: SMYD3, ZMYND1, ZNFN3A1 EC: 2.1.1.43 (PDB Primary Data), 2.1.1.354 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H7B4 (Homo sapiens) Explore Q9H7B4  Go to UniProtKB:  Q9H7B4
PHAROS:  Q9H7B4 GTEx:  ENSG00000185420

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	E [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
ZN	B [auth A], C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.208 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.809	α = 90
b = 65.923	β = 90
c = 108.102	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-14 
Deposition Author(s): Lam, R., Dombrovski, L., Li, Y., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Min, J., Wu, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2010-04-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary