Research workbench
SETD3 in complex with an actin peptide with HIS73 replaced with lysine
Analyse SETD3 in complex with an actin peptide with HIS73 replaced with lysine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OX3
- Type
- protein
- Length
- 1,004 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin peptide; Histone-lysine N-methyltransferase SETD3
- EC
- 2.1.1.85
- UniProt
- C9JUM1, Q86TU7
- Ligands
- SAH
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Y, Z | Actin peptide | protein | 19 | 0% helix, 5% strand | C9JUM1 |
| A | Histone-lysine N-methyltransferase SETD3 (EC 2.1.1.85) | protein | 483 | 51% helix, 12% strand | Q86TU7 |
| B | Histone-lysine N-methyltransferase SETD3 (EC 2.1.1.85) | protein | 483 | 50% helix, 13% strand | Q86TU7 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains Y, A, Z, B
- EDO · 1,2-ethanediol · additive · 34 copies · chains A, Y, B, Z
- GOL · Glycerol · additive · 5 copies · chains Y, A
- ACT · Acetate ion · additive · chains A
- PGE · Triethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1060 | 0.83 | 0.84 | 121 | SAH, GOL, EDO, PGE |
| 2 | 255 | 0.58 | 0.79 | 48 | EDO |
| 3 | 190 | 0.55 | 0.79 | 33 | EDO |
| 4 | 98 | 0.52 | 0.84 | 28 | empty |
| 5 | 123 | 0.47 | 0.79 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1261 Ų buried · 18 hydrogen bonds · protein-protein
- Y–A · 1240 Ų buried · 22 hydrogen bonds · protein-protein
- Z–B · 1221 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6OX3 · SETD3 in Complex with an Actin Peptide with His73 Replaced with Lysine · the same entry in another collection · chain Z against Z, 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
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 C9JUM1
- Every structure of UniProt Q86TU7
- Elsewhere: RCSB PDB 6OX3 · PDBe 6OX3 · UniProt C9JUM1 · UniProt Q86TU7
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