MolNFT v1 · #134756 · protein
Crystal structure of HSETD8 in complex with histone H4K20 norleucine mutant peptide and S-adenosylmethionine
5TEG · N-lysine methyltransferase KMT5A: “Crystal structure of HSETD8 in complex with histone H4K20 norleucine mutant peptide and S-adenosylmethionine”. X-ray diffraction, 1 ligand (SAM), 3 pockets (best druggability 0.49). MolNFT v1…
- PDB
- 5TEG
- Type
- protein
- Length
- 333 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-lysine methyltransferase KMT5A; Histone H4 mutant peptide with H4K20NORLEUCINE
- EC
- 2.1.1.-, 2.1.1.43
- UniProt
- Q9NQR1
- Ligands
- SAM
- Pockets
- 3 · best druggability 0.49
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-lysine methyltransferase KMT5A (EC 2.1.1.-, 2.1.1.43) | protein | 160 | 26% helix, 35% strand | Q9NQR1 |
| B | N-lysine methyltransferase KMT5A (EC 2.1.1.-, 2.1.1.43) | protein | 158 | 27% helix, 35% strand | Q9NQR1 |
| D | Histone H4 mutant peptide with H4K20NORLEUCINE | protein | 8 | 0% helix, 25% strand | — |
| E | Histone H4 mutant peptide with H4K20NORLEUCINE | protein | 7 | 0% helix, 29% strand | — |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, D, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 171 | 0.49 | 0.77 | 27 | SAM |
| 2 | 169 | 0.45 | 0.75 | 27 | SAM |
| 3 | 66 | 0.31 | 0.76 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–D · 875 Ų buried · 13 hydrogen bonds · protein-protein
- B–E · 767 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 382 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 5TEG · Crystal structure of hSETD8 in complex with histone H4K20 norleucine mutant peptide and… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NQR1 · AlphaFold monomer V2.0 prediction for N-lysine methyltransferase KMT5A (Q9NQR1) · a predicted model of the same protein · chain A 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 5TEG · PDBe 5TEG · UniProt Q9NQR1
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