Research workbench
SETD3 in complex with an actin peptide with target histidine partially methylated
Analyse SETD3 in complex with an actin peptide with target histidine partially… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OX1
- Type
- protein
- Length
- 997 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin, cytoplasmic 1; Histone-lysine N-methyltransferase SETD3
- EC
- 2.1.1.85
- UniProt
- P60709, Q86TU7
- Ligands
- SAH
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Y, Z | Actin, cytoplasmic 1 | protein | 15 | 0% helix, 7% strand | P60709 |
| A | Histone-lysine N-methyltransferase SETD3 (EC 2.1.1.85) | protein | 483 | 51% helix, 13% strand | Q86TU7 |
| B | Histone-lysine N-methyltransferase SETD3 (EC 2.1.1.85) | protein | 484 | 51% helix, 13% strand | Q86TU7 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains Y, A, B, Z
- EDO · 1,2-ethanediol · additive · 22 copies · chains A, B, Y
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1190 | 0.83 | 0.84 | 131 | SAH, EDO |
| 2 | 183 | 0.57 | 0.81 | 34 | EDO |
| 3 | 196 | 0.50 | 0.76 | 24 | EDO |
| 4 | 98 | 0.48 | 0.81 | 22 | empty |
| 5 | 69 | 0.42 | 0.81 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1284 Ų buried · 18 hydrogen bonds · protein-protein
- B–Z · 1086 Ų buried · 17 hydrogen bonds · protein-protein
- Y–A · 1086 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 6OX1 · SETD3 in Complex with an Actin Peptide with Target Histidine Partially Methylated · the same entry in another collection · chain Y against Y, TM-score 1.00
- Q86TU7 · AlphaFold monomer V2.0 prediction for actin-histidine N-methyltransferase (Q86TU7) · a predicted model of the same protein · chain A 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 Y against A, TM-score 0.24
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 6OX1 · PDBe 6OX1 · UniProt P60709 · UniProt Q86TU7
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