Research workbench
A SETD3 mutant (N255A) in complex with an actin peptide
Analyse A SETD3 mutant (N255A) in complex with an actin peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OX4
- Type
- protein
- Length
- 996 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin peptide; Actin-histidine N-methyltransferase
- EC
- 2.1.1.85
- UniProt
- P60709, Q86TU7
- Ligands
- SAH
- Pockets
- 14 · 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, 7% strand | P60709 |
| A, B | Actin-histidine N-methyltransferase (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 · 32 copies · chains Y, A, B
- GOL · Glycerol · additive · 3 copies · chains A
- ACT · Acetate ion · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1049 | 0.83 | 0.84 | 115 | SAH, EDO, GOL |
| 2 | 260 | 0.57 | 0.78 | 51 | EDO |
| 3 | 114 | 0.54 | 0.83 | 20 | EDO |
| 4 | 134 | 0.52 | 0.81 | 19 | empty |
| 5 | 89 | 0.45 | 0.81 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1242 Ų buried · 14 hydrogen bonds · protein-protein
- Z–B · 1081 Ų buried · 17 hydrogen bonds · protein-protein
- Y–A · 1045 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6OX4 · A SETD3 Mutant (N255A) in Complex with an Actin Peptide · 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 0.26
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 6OX4 · PDBe 6OX4 · UniProt P60709 · UniProt Q86TU7
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