Research workbench
Structure of SETD3 bound to sah and unmodified actin
Analyse Structure of SETD3 bound to sah and unmodified actin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ICV
- Type
- protein
- Length
- 993 residues
- Chains
- 4
- 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
- 10 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase SETD3 (EC 2.1.1.43) | protein | 480 | 51% helix, 13% strand | Q86TU7 |
| C, D | Actin, cytoplasmic 1 | protein | 17 | 0% helix, 6% strand | P60709 |
| B | Histone-lysine N-methyltransferase SETD3 (EC 2.1.1.43) | protein | 479 | 51% helix, 13% strand | Q86TU7 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1029 | 0.83 | 0.84 | 129 | SAH |
| 2 | 186 | 0.55 | 0.79 | 34 | empty |
| 3 | 161 | 0.52 | 0.79 | 29 | empty |
| 4 | 79 | 0.49 | 0.83 | 18 | empty |
| 5 | 64 | 0.39 | 0.79 | 14 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1188 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1185 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1058 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6ICV · Structure of SETD3 bound to SAH and unmodified actin · the same entry in another collection · chain D against D, TM-score 1.00
- Q86TU7 · AlphaFold monomer V2.0 prediction for actin-histidine N-methyltransferase (Q86TU7) · a predicted model of the same protein · chain B against A, TM-score 1.00
- P60709 · AlphaFold monomer V2.0 prediction for actin, cytoplasmic 1 (P60709) · a predicted model of the same protein · chain D against A, TM-score 0.21
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 6ICV · PDBe 6ICV · UniProt Q86TU7 · UniProt P60709
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