Research workbench
SETD3, a Histidine Methyltransferase, in Complex with an Actin Peptide and SAH, P21 Crystal Form
Analyse SETD3, a Histidine Methyltransferase, in Complex with an Actin Peptide and SAH… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MBJ
- Type
- protein
- Length
- 994 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.78
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Actin Peptide; Histone-lysine N-methyltransferase setd3
- EC
- 2.1.1.43
- UniProt
- P60709, Q86TU7
- Ligands
- SAH
- Pockets
- 14 · best druggability 0.83
Structure
x-ray diffraction · resolution 1.78 · 3 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Y, Z | Actin Peptide | protein | 15 | 0% helix, 7% strand | P60709 |
| A | Histone-lysine N-methyltransferase setd3 (EC 2.1.1.43) | protein | 481 | 51% helix, 13% strand | Q86TU7 |
| B | Histone-lysine N-methyltransferase setd3 (EC 2.1.1.43) | protein | 483 | 50% helix, 13% strand | Q86TU7 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains Y, A, Z, B
- EDO · 1,2-ethanediol · additive · 35 copies · chains Y, A, B, Z
- GOL · Glycerol · additive · 3 copies · chains A
- ACT · Acetate ion · additive · 2 copies · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1139 | 0.83 | 0.84 | 109 | SAH, EDO, GOL |
| 2 | 131 | 0.60 | 0.85 | 29 | empty |
| 3 | 186 | 0.56 | 0.80 | 33 | EDO |
| 4 | 114 | 0.55 | 0.83 | 20 | empty |
| 5 | 98 | 0.51 | 0.82 | 22 | EDO |
Interfaces
3 interfaces between chains.
- A–B · 1294 Ų buried · 21 hydrogen bonds · protein-protein
- Z–B · 1080 Ų buried · 18 hydrogen bonds · protein-protein
- Y–A · 1076 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6MBJ · SETD3, a histidine methyltransferase, in complex with an actin peptide and sah, P21… · 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 B 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 6MBJ · PDBe 6MBJ · UniProt P60709 · UniProt Q86TU7
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