MolNFT v1 · #166944 · protein
SETD3 wt in complex with an actin peptide with HIS73 replaced with glutamine
6V63 · Actin, cytoplasmic 1: “SETD3 wt in complex with an actin peptide with HIS73 replaced with glutamine”. X-ray diffraction, 1 ligand (SAH), 14 pockets (best druggability 0.83). MolNFT v1 #166944 on GenesisL1: 3D structure, binding…
- 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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