MolNFT v1 · #78891 · protein
Crystal structure of human set domain-containing PROTEIN3
3SMT · Histone-lysine N-methyltransferase SETD3: “Crystal structure of human set domain-containing PROTEIN3”. X-ray diffraction, 3 ligands (SAM, ARS, UNX), 4 pockets (best druggability 0.71). MolNFT v1 #78891 on GenesisL1: 3D structure…
- PDB
- 3SMT
- Type
- protein
- Length
- 465 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase SETD3
- EC
- 2.1.1.43
- UniProt
- Q86TU7
- Ligands
- SAM, ARS, UNX
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase SETD3 (EC 2.1.1.43) | protein | 465 | 48% helix, 14% strand | Q86TU7 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · chains A
- ARS · Arsenic · metal · 2 copies · chains A
- UNX · Unknown atom or ion · ion · 11 copies · chains A
- ACT · Acetate ion · additive · 2 copies · chains A
- PG4 · Tetraethylene glycol · additive · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 591 | 0.71 | 0.79 | 67 | SAM, ARS, UNX |
| 2 | 54 | 0.47 | 0.85 | 18 | UNX |
| 3 | 55 | 0.32 | 0.77 | 16 | empty |
| 4 | 57 | 0.28 | 0.74 | 13 | empty |
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 3SMT · Crystal structure of human SET domain-containing protein3 · the same entry in another collection · chain A against A, TM-score 1.00
- Q86TU7 · AlphaFold monomer V2.0 prediction for actin-histidine N-methyltransferase (Q86TU7) · 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 Q86TU7
- Elsewhere: RCSB PDB 3SMT · PDBe 3SMT · UniProt Q86TU7
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