MolNFT v1 · #136727 · protein
Crystal structure of human SETD2 set-domain in complex with H3K36M peptide and SAM
5V21 · Histone-lysine N-methyltransferase SETD2: “Crystal structure of human SETD2 set-domain in complex with H3K36M peptide and SAM”. X-ray diffraction, 2 ligands (SAM, ZN), 2 pockets (best druggability 0.64). MolNFT v1 #136727 on…
- PDB
- 5V21
- Type
- protein
- Length
- 260 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase SETD2; Histone H3K36M peptide
- EC
- 2.1.1.43
- UniProt
- Q9BYW2
- Ligands
- SAM, ZN
- Pockets
- 2 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase SETD2 (EC 2.1.1.43) | protein | 245 | 21% helix, 28% strand | Q9BYW2 |
| B | Histone H3K36M peptide | protein | 15 | 0% helix, 20% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 202 | 0.64 | 0.83 | 32 | SAM |
| 2 | 75 | 0.48 | 0.83 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1095 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 5V21 · Crystal structure of human SETD2 SET-domain in complex with H3K36M peptide and SAM · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BYW2 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase SETD2 (Q9BYW2) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 Q9BYW2
- Elsewhere: RCSB PDB 5V21 · PDBe 5V21 · UniProt Q9BYW2
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