MolNFT v1 · #87230 · protein
A novel route to product specificity in the SUV4-20 family of histone H4K20 methyltransferases
4BUP · Histone-lysine N-methyltransferase SUV420H1: “A novel route to product specificity in the SUV4-20 family of histone H4K20 methyltransferases”. X-ray diffraction, 2 ligands (SAM, ZN), 10 pockets (best druggability 0.67). MolNFT v1…
- PDB
- 4BUP
- Type
- protein
- Length
- 469 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase SUV420H1
- EC
- 2.1.1.43
- UniProt
- Q3U8K7
- Ligands
- SAM, ZN
- Pockets
- 10 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase SUV420H1 (EC 2.1.1.43) | protein | 232 | 34% helix, 22% strand | Q3U8K7 |
| B | Histone-lysine N-methyltransferase SUV420H1 (EC 2.1.1.43) | protein | 237 | 38% helix, 22% strand | Q3U8K7 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 321 | 0.67 | 0.82 | 38 | SAM, GOL |
| 2 | 232 | 0.60 | 0.80 | 32 | SAM |
| 3 | 113 | 0.47 | 0.79 | 17 | empty |
| 4 | 68 | 0.43 | 0.81 | 14 | empty |
| 5 | 99 | 0.42 | 0.78 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 366 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4BUP · A novel route to product specificity in the Suv4-20 family of histone H4K20… · the same entry in another collection · chain B against B, TM-score 1.00
- Q3U8K7 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase KMT5B (Q3U8K7) · a predicted model of the same protein · chain B 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 Q3U8K7
- Elsewhere: RCSB PDB 4BUP · PDBe 4BUP · UniProt Q3U8K7
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