MolNFT v1 · #168553 · protein
SETD3 in complex with an actin peptide with HIS73 replaced with methionine
6WK1 · Actin, cytoplasmic 2: “SETD3 in complex with an actin peptide with HIS73 replaced with methionine”. X-ray diffraction, 1 ligand (SAH), 13 pockets (best druggability 0.82). MolNFT v1 #168553 on GenesisL1: 3D structure, binding sites…
- 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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