Research workbench
Structure of CLR4 mutant - F256A/F310A/F427A bound to sah
Analyse Structure of CLR4 mutant - F256A/F310A/F427A bound to sah in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Z2A
- Type
- protein
- Length
- 559 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase, H3 lysine-9 specific
- EC
- 2.1.1.355
- UniProt
- O60016
- Ligands
- SAH, ZN, MG
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase, H3 lysine-9 specific (EC 2.1.1.355) | protein | 283 | 12% helix, 22% strand | O60016 |
| B | Histone-lysine N-methyltransferase, H3 lysine-9 specific (EC 2.1.1.355) | protein | 276 | 13% helix, 22% strand | O60016 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 8 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 320 | 0.71 | 0.84 | 42 | SAH |
| 2 | 255 | 0.70 | 0.85 | 40 | SAH |
| 3 | 252 | 0.57 | 0.78 | 38 | empty |
| 4 | 261 | 0.56 | 0.77 | 34 | empty |
| 5 | 221 | 0.47 | 0.74 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 291 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6Z2A · Structure of Clr4 mutant - F256A/F310A/F427A bound to SAH · the same entry in another collection · chain A against A, TM-score 1.00
- O60016 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase, H3 lysine-9… · a predicted model of the same protein · chain B against A, TM-score 0.97
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt O60016
- Elsewhere: RCSB PDB 6Z2A · PDBe 6Z2A · UniProt O60016
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