MolNFT v1 · #159665 · protein
SETD3IN complex with an actin peptide with the target histidine fully methylated
6OX2: “SETD3IN complex with an actin peptide with the target histidine fully methylated”. X-ray diffraction, 1 ligand (SAH), 13 pockets (best druggability 0.83). MolNFT v1 #159665 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6OX2
- Type
- protein
- Length
- 996 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
- P60709, Q86TU7
- Ligands
- SAH
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Y, Z | Actin peptide | protein | 15 | 0% helix, 0% strand | P60709 |
| A, B | Histone-lysine N-methyltransferase SETD3 (EC 2.1.1.85) | protein | 483 | 51% helix, 12% strand | Q86TU7 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains Y, A, Z, B
- EDO · 1,2-ethanediol · additive · 23 copies · chains A, Y, B
- GOL · Glycerol · 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 | 1124 | 0.83 | 0.84 | 115 | SAH, EDO, GOL |
| 2 | 140 | 0.59 | 0.84 | 30 | empty |
| 3 | 146 | 0.58 | 0.83 | 31 | empty |
| 4 | 182 | 0.57 | 0.81 | 33 | EDO |
| 5 | 106 | 0.47 | 0.80 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1256 Ų buried · 17 hydrogen bonds · protein-protein
- Y–A · 1095 Ų buried · 17 hydrogen bonds · protein-protein
- Z–B · 1093 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 6OX2 · SETD3in Complex with an Actin Peptide with the Target Histidine Fully Methylated · the same entry in another collection · chain B against B, 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 Z 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 P60709
- Every structure of UniProt Q86TU7
- Elsewhere: RCSB PDB 6OX2 · PDBe 6OX2 · UniProt P60709 · UniProt Q86TU7
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