Research workbench
Structure of the S. pombe CLR4 catalytic domain bound to SAM
Analyse Structure of the S. pombe CLR4 catalytic domain bound to SAM in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BP4
- Type
- protein
- Length
- 550 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
- 2.1.1.43
- UniProt
- O60016
- Ligands
- SAM, ZN
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Histone-lysine N-methyltransferase, H3 lysine-9 specific (EC 2.1.1.43) | protein | 282 | 13% helix, 23% strand | O60016 |
| A | Histone-lysine N-methyltransferase, H3 lysine-9 specific (EC 2.1.1.43) | protein | 268 | 12% helix, 24% strand | O60016 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains B, A
- ZN · Zinc ion · metal · 8 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1009 | 0.77 | 0.79 | 91 | SAM |
| 2 | 322 | 0.62 | 0.79 | 35 | SAM |
| 3 | 301 | 0.58 | 0.77 | 39 | empty |
| 4 | 259 | 0.58 | 0.78 | 36 | empty |
| 5 | 138 | 0.48 | 0.77 | 23 | empty |
Interfaces
1 interface between chains.
- B–A · 463 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6BP4 · Structure of the S. pombe Clr4 catalytic domain bound to SAM · the same entry in another collection · chain B against B, 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 A against A, TM-score 0.98
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 6BP4 · PDBe 6BP4 · UniProt O60016
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