› 4i51

X-ray diffraction
1.9Å resolution

Methyltransferase domain of HUMAN EUCHROMATIC HISTONE METHYLTRANSFERASE 1, mutant Y1211A

Released:
DOI: 10.2210/pdb4i51/pdb
PDB entry 4i51 coloured by chain, front view.
PDB entry 4i51 coloured by chain, side view.
PDB entry 4i51 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Defining efficient enzyme-cofactor pairs for bioorthogonal profiling of protein methylation.
Islam K, Chen Y, Wu H, Bothwell IR, Blum GJ, Zeng H, Dong A, Zheng W, Min J, Deng H, Luo M
Proc Natl Acad Sci U S A 110 16778-83 (2013)
PMID: 24082136

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + a [histone H3]-L-lysine(9) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(9)
Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
PDBe Complex ID:
PDB-CPX-159456 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Histone-lysine N-methyltransferase EHMT1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 286 amino acids
Theoretical weight: 32.8 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9H9B1 (Residues: 982-1266; Coverage: 22%)
Gene names: EHMT1, EUHMTASE1, GLP, KIAA1876, KMT1D
Sequence domains:
Structure domains: SET domain
Histone H3.1 Chains: C, D
Molecule details ›
Chains: C, D
Length: 9 amino acids
Theoretical weight: 1.05 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P68431 (Residues: 4-12; Coverage: 7%)
Gene names: H3C1, H3C10, H3C11, H3C12, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3FA, H3FB, H3FC HIST1H3C, H3FD, H3FF, H3FH, H3FI, H3FJ, H3FK, H3FL, HIST1H3A, HIST1H3B, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J
UNKNOWN PEPTIDE Chain: K
Molecule details ›
Chain: K
Length: 13 amino acids
Theoretical weight: 1.12 KDa

Ligands and Environments

4 bound ligands:
Ligand SAH 2 x SAH
Ligand ZN 8 x ZN
Ligand GOL 3 x GOL
Ligand UNX 9 x UNX
1 modified residue:
Ligand LDH 2 x LDH

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P212121
Unit cell:
a: 83.497Å b: 83.8Å c: 95.052Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.171 0.171 0.195
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

19 review citations

Structure-based virtual screening for drug discovery: principles, applications and recent advances.
Lionta et al. (2014)
18 more

3 mentions without citation

Metformin Is a Direct SIRT1-Activating Compound: Computational Modeling and Experimental Validation.
Cuyàs et al. (2018)
2 more