MolNFT v1 · #29826 · protein
Crystal structure of HSET8 in ternary complex with H4 peptide (16-24) and adohcy
1ZKK · Histone-lysine N-methyltransferase, H4 lysine-20 specific: “Crystal structure of HSET8 in ternary complex with H4 peptide (16-24) and adohcy”. X-ray diffraction, 1 ligand (SAH), 10 pockets (best druggability 0.74). MolNFT v1 #29826…
- PDB
- 1ZKK
- Type
- protein
- Length
- 676 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase, H4 lysine-20 specific; Peptide corresponding to…
- EC
- 2.1.1.43
- UniProt
- Q9NQR1
- Ligands
- SAH
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Histone-lysine N-methyltransferase, H4 lysine-20 specific (EC 2.1.1.43) | protein | 160 | 26% helix, 35% strand | Q9NQR1 |
| B, D | Histone-lysine N-methyltransferase, H4 lysine-20 specific (EC 2.1.1.43) | protein | 161 | 26% helix, 34% strand | Q9NQR1 |
| E, H | Peptide corresponding to residues 15-24 of histone H4 | protein | 8 | 0% helix, 25% strand | — |
| F, G | Peptide corresponding to residues 15-24 of histone H4 | protein | 9 | 0% helix, 22% strand | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, E, G, B, F, C, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 662 | 0.74 | 0.80 | 63 | SAH |
| 2 | 648 | 0.73 | 0.80 | 59 | SAH |
| 3 | 639 | 0.72 | 0.79 | 60 | SAH |
| 4 | 231 | 0.53 | 0.77 | 28 | empty |
| 5 | 61 | 0.43 | 0.82 | 20 | empty |
Interfaces
10 interfaces between chains.
- B–F · 863 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 832 Ų buried · 14 hydrogen bonds · protein-protein
- D–H · 827 Ų buried · 15 hydrogen bonds · protein-protein
- C–G · 813 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 514 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1ZKK · Crystal structure of hSET8 in ternary complex with H4 peptide (16-24) and AdoHcy · the same entry in another collection · chain H against H, TM-score 1.00
- Q9NQR1 · AlphaFold monomer V2.0 prediction for N-lysine methyltransferase KMT5A (Q9NQR1) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q9NQR1
- Elsewhere: RCSB PDB 1ZKK · PDBe 1ZKK · UniProt Q9NQR1
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