MolNFT v1 · #86030 · protein
The structure of the SUV4-20H2 ternary complex with histone H4
4AU7 · Histone-lysine N-methyltransferase SUV420H2: “The structure of the SUV4-20H2 ternary complex with histone H4”. X-ray diffraction, 2 ligands (SAH, ZN), 7 pockets (best druggability 0.65). MolNFT v1 #86030 on GenesisL1: 3D structure…
- PDB
- 4AU7
- Type
- protein
- Length
- 461 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase SUV420H2; Histone H4 peptide
- EC
- 2.1.1.43
- UniProt
- Q6Q783, P62806
- Ligands
- SAH, ZN
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase SUV420H2 (EC 2.1.1.43) | protein | 243 | 35% helix, 21% strand | Q6Q783 |
| B | Histone-lysine N-methyltransferase SUV420H2 (EC 2.1.1.43) | protein | 209 | 38% helix, 22% strand | Q6Q783 |
| C | Histone H4 peptide | protein | 9 | 0% helix, 33% strand | P62806 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A, C
- ZN · Zinc ion · metal · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 16 copies · chains A, C, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 352 | 0.65 | 0.80 | 34 | SAH, EDO |
| 2 | 234 | 0.54 | 0.77 | 33 | EDO |
| 3 | 196 | 0.49 | 0.75 | 27 | empty |
| 4 | 84 | 0.42 | 0.79 | 20 | EDO |
| 5 | 98 | 0.40 | 0.77 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–C · 838 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 288 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 182 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (methylation).
Compared structures
- 4AU7 · The structure of the Suv4-20h2 ternary complex with histone H4 · the same entry in another collection · chain A against A, TM-score 1.00
- Q6Q783 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase KMT5C (Q6Q783) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P62806 · AlphaFold monomer V2.0 prediction for histone H4 (P62806) · a predicted model of the same protein · chain C against A, TM-score 0.29
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 Q6Q783
- Every structure of UniProt P62806
- Elsewhere: RCSB PDB 4AU7 · PDBe 4AU7 · UniProt Q6Q783 · UniProt P62806
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