Research workbench
Crystal structure of methyltransferase domain of human set domain- containing protein 2 compound: pr-snf
Analyse Crystal structure of methyltransferase domain of human set domain- containing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FMU
- Type
- protein
- Length
- 235 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase SETD2
- EC
- 2.1.1.43
- UniProt
- Q9BYW2
- Ligands
- 0UM, ZN, UNX
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase SETD2 (EC 2.1.1.43) | protein | 235 | 20% helix, 26% strand | Q9BYW2 |
Ligands and binding sites
- 0UM · (2S,5S)-2-amino-6-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]-5-(propylamino)hexanoic acid · ligand · chains A
- ZN · Zinc ion · metal · 3 copies · chains A
- UNX · Unknown atom or ion · ion · 13 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 187 | 0.66 | 0.85 | 33 | 0UM |
| 2 | 135 | 0.56 | 0.82 | 20 | empty |
| 3 | 115 | 0.46 | 0.78 | 16 | UNX |
| 4 | 68 | 0.35 | 0.76 | 18 | UNX |
Compared structures
- 4FMU · Crystal structure of Methyltransferase domain of human SET domain-containing protein 2… · 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 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 Q9BYW2
- Elsewhere: RCSB PDB 4FMU · PDBe 4FMU · UniProt Q9BYW2
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