MolNFT v1 · #153317 · protein
Crystal structure of SETD3 bound to actin peptide and sfg
6JAT · Histone-lysine N-methyltransferase SETD3: “Crystal structure of SETD3 bound to actin peptide and sfg”. X-ray diffraction, 2 ligands (SFG, SO4), 12 pockets (best druggability 0.70). MolNFT v1 #153317 on GenesisL1: 3D structure…
- PDB
- 6JAT
- Type
- protein
- Length
- 978 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase SETD3; Actin, gamma-enteric smooth muscle
- EC
- 2.1.1.43
- UniProt
- Q86TU7, P63267
- Ligands
- SFG, SO4
- Pockets
- 12 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase SETD3 (EC 2.1.1.43) | protein | 475 | 51% helix, 13% strand | Q86TU7 |
| B | Actin, gamma-enteric smooth muscle | protein | 16 | 0% helix, 6% strand | P63267 |
| C | Histone-lysine N-methyltransferase SETD3 (EC 2.1.1.43) | protein | 472 | 50% helix, 13% strand | Q86TU7 |
| D | Actin, gamma-enteric smooth muscle | protein | 15 | 0% helix, 7% strand | P63267 |
Ligands and binding sites
- SFG · Sinefungin · ligand · 2 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 5 copies · chains A, C
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 201 | 0.70 | 0.87 | 29 | SFG |
| 2 | 189 | 0.69 | 0.87 | 26 | SFG |
| 3 | 203 | 0.67 | 0.86 | 39 | empty |
| 4 | 95 | 0.60 | 0.88 | 29 | empty |
| 5 | 66 | 0.48 | 0.85 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1319 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1169 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1168 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6JAT · Crystal structure of SETD3 bound to Actin peptide and SFG · 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 C against A, TM-score 1.00
- P63267 · AlphaFold monomer V2.0 prediction for actin, gamma-enteric smooth muscle (P63267) · a predicted model of the same protein · chain D against A, TM-score 0.25
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
- Every structure of UniProt P63267
- Elsewhere: RCSB PDB 6JAT · PDBe 6JAT · UniProt Q86TU7 · UniProt P63267
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