MolNFT v1 · #159664 · protein
SETD3 in complex with an actin peptide with target histidine partially methylated
6OX1 · Actin, cytoplasmic 1: “SETD3 in complex with an actin peptide with target histidine partially methylated”. X-ray diffraction, 1 ligand (SAH), 12 pockets (best druggability 0.83). MolNFT v1 #159664 on GenesisL1: 3D structure, binding…
- PDB
- 6OX1
- Type
- protein
- Length
- 997 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin, cytoplasmic 1; Histone-lysine N-methyltransferase SETD3
- EC
- 2.1.1.85
- UniProt
- P60709, Q86TU7
- Ligands
- SAH
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Y, Z | Actin, cytoplasmic 1 | protein | 15 | 0% helix, 7% strand | P60709 |
| A | Histone-lysine N-methyltransferase SETD3 (EC 2.1.1.85) | protein | 483 | 51% helix, 13% strand | Q86TU7 |
| B | Histone-lysine N-methyltransferase SETD3 (EC 2.1.1.85) | protein | 484 | 51% helix, 13% strand | Q86TU7 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains Y, A, B, Z
- EDO · 1,2-ethanediol · additive · 22 copies · chains A, B, Y
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1190 | 0.83 | 0.84 | 131 | SAH, EDO |
| 2 | 183 | 0.57 | 0.81 | 34 | EDO |
| 3 | 196 | 0.50 | 0.76 | 24 | EDO |
| 4 | 98 | 0.48 | 0.81 | 22 | empty |
| 5 | 69 | 0.42 | 0.81 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1284 Ų buried · 18 hydrogen bonds · protein-protein
- B–Z · 1086 Ų buried · 17 hydrogen bonds · protein-protein
- Y–A · 1086 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 6OX1 · SETD3 in Complex with an Actin Peptide with Target Histidine Partially Methylated · the same entry in another collection · chain Y against Y, 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
- P60709 · AlphaFold monomer V2.0 prediction for actin, cytoplasmic 1 (P60709) · a predicted model of the same protein · chain Y against A, TM-score 0.24
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 6OX1 · PDBe 6OX1 · UniProt P60709 · UniProt Q86TU7
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