MolNFT v1 · #152282 · protein
Structure of SETD3 bound to sah and methylated actin
6ICT · Histone-lysine N-methyltransferase SETD3: “Structure of SETD3 bound to sah and methylated actin”. X-ray diffraction, 1 ligand (SAH), 20 pockets (best druggability 0.83). MolNFT v1 #152282 on GenesisL1: 3D structure, binding sites…
- PDB
- 6ICT
- Type
- protein
- Length
- 1,989 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase SETD3; Actin, cytoplasmic 1
- EC
- 2.1.1.43
- UniProt
- Q86TU7, P60709
- Ligands
- SAH
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase SETD3 (EC 2.1.1.43) | protein | 478 | 51% helix, 13% strand | Q86TU7 |
| B | Histone-lysine N-methyltransferase SETD3 (EC 2.1.1.43) | protein | 480 | 51% helix, 13% strand | Q86TU7 |
| C, D | Histone-lysine N-methyltransferase SETD3 (EC 2.1.1.43) | protein | 479 | 51% helix, 13% strand | Q86TU7 |
| E, H | Actin, cytoplasmic 1 | protein | 19 | 21% helix, 5% strand | P60709 |
| G | Actin, cytoplasmic 1 | protein | 18 | 0% helix, 6% strand | P60709 |
| I | Actin, cytoplasmic 1 | protein | 17 | 0% helix, 6% strand | P60709 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, E, B, G, C, H, D, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1160 | 0.83 | 0.84 | 115 | SAH |
| 2 | 602 | 0.72 | 0.80 | 59 | empty |
| 3 | 294 | 0.72 | 0.86 | 44 | empty |
| 4 | 225 | 0.72 | 0.87 | 32 | SAH |
| 5 | 237 | 0.71 | 0.87 | 31 | SAH |
Interfaces
9 interfaces between chains.
- C–H · 1325 Ų buried · 19 hydrogen bonds · protein-protein
- A–E · 1277 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1271 Ų buried · 17 hydrogen bonds · protein-protein
- D–I · 1213 Ų buried · 23 hydrogen bonds · protein-protein
- B–G · 1207 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (methylation).
Compared structures
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 P60709
- Elsewhere: RCSB PDB 6ICT · PDBe 6ICT · UniProt Q86TU7 · UniProt P60709
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