Research workbench
SETD3 wt in complex with an actin peptide with HIS73 replaced with glutamine
Analyse SETD3 wt in complex with an actin peptide with HIS73 replaced with glutamine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6V63
- Type
- protein
- Length
- 1,005 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin, cytoplasmic 1; Actin-histidine N-methyltransferase
- EC
- 2.1.1.85
- UniProt
- C9JUM1, Q86TU7
- Ligands
- SAH
- Pockets
- 14 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Y, Z | Actin, cytoplasmic 1 | protein | 19 | 0% helix, 5% strand | C9JUM1 |
| A | Actin-histidine N-methyltransferase (EC 2.1.1.85) | protein | 484 | 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 · 36 copies · chains A, Y, B, Z
- GOL · Glycerol · additive · 2 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
14 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1106 | 0.83 | 0.84 | 127 | SAH, EDO |
| 2 | 243 | 0.61 | 0.81 | 43 | EDO |
| 3 | 91 | 0.49 | 0.82 | 19 | empty |
| 4 | 130 | 0.47 | 0.78 | 27 | empty |
| 5 | 91 | 0.47 | 0.81 | 22 | EDO |
Interfaces
3 interfaces between chains.
- A–B · 1302 Ų buried · 21 hydrogen bonds · protein-protein
- Y–A · 1226 Ų buried · 23 hydrogen bonds · protein-protein
- Z–B · 1204 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 6V63 · SETD3 WT in Complex with an Actin Peptide with His73 Replaced with Glutamine · 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
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 C9JUM1
- Every structure of UniProt Q86TU7
- Elsewhere: RCSB PDB 6V63 · PDBe 6V63 · UniProt C9JUM1 · UniProt Q86TU7
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