Research workbench
SETD3 in complex with an actin peptide with HIS73 replaced with methionine
Analyse SETD3 in complex with an actin peptide with HIS73 replaced with methionine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WK1
- Type
- protein
- Length
- 1,004 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin, cytoplasmic 2; Actin-histidine N-methyltransferase
- EC
- 2.1.1.85
- UniProt
- P63261, Q86TU7
- Ligands
- SAH
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Y, Z | Actin, cytoplasmic 2 | protein | 19 | 0% helix, 5% strand | P63261 |
| A | Actin-histidine N-methyltransferase (EC 2.1.1.85) | protein | 483 | 51% helix, 12% strand | Q86TU7 |
| B | Actin-histidine N-methyltransferase (EC 2.1.1.85) | protein | 483 | 51% helix, 13% strand | Q86TU7 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 46 copies · chains Y, A, B, Z
- GOL · Glycerol · additive · 6 copies · chains Y, A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 918 | 0.82 | 0.84 | 108 | SAH, EDO |
| 2 | 274 | 0.62 | 0.80 | 47 | EDO |
| 3 | 116 | 0.56 | 0.84 | 28 | EDO |
| 4 | 138 | 0.48 | 0.78 | 26 | empty |
| 5 | 149 | 0.47 | 0.77 | 29 | EDO |
Interfaces
3 interfaces between chains.
- A–B · 1268 Ų buried · 17 hydrogen bonds · protein-protein
- Y–A · 1248 Ų buried · 22 hydrogen bonds · protein-protein
- Z–B · 1214 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6WK1 · SETD3 in Complex with an Actin Peptide with His73 Replaced with Methionine · 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 A against A, TM-score 1.00
- P63261 · AlphaFold monomer V2.0 prediction for actin, cytoplasmic 2 (P63261) · a predicted model of the same protein · chain Y against A, TM-score 0.19
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 P63261
- Every structure of UniProt Q86TU7
- Elsewhere: RCSB PDB 6WK1 · PDBe 6WK1 · UniProt P63261 · UniProt Q86TU7
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