MolNFT v1 · #156668 · protein
SETD3, a histidine methyltransferase, in complex with an actin peptide and sah, first P212121 crystal form
6MBK: “SETD3, a histidine methyltransferase, in complex with an actin peptide and sah, first P212121 crystal form”. X-ray diffraction, 2 ligands (SAH, SO4), 16 pockets (best druggability 0.71). MolNFT v1 #156668 on GenesisL1: 3D structure…
- PDB
- 6MBK
- Type
- protein
- Length
- 994 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin peptide; Histone-lysine N-methyltransferase SETD3
- EC
- 2.1.1.43
- UniProt
- P60709, Q86TU7
- Ligands
- SAH, SO4
- Pockets
- 16 · best druggability 0.71
Structure
x-ray diffraction · 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 | 483 | 50% helix, 13% strand | Q86TU7 |
| B | Histone-lysine N-methyltransferase SETD3 (EC 2.1.1.43) | protein | 481 | 52% helix, 13% strand | Q86TU7 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains Y, A, Z, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 14 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 215 | 0.71 | 0.87 | 28 | SAH, GOL |
| 2 | 200 | 0.70 | 0.87 | 31 | SAH |
| 3 | 224 | 0.68 | 0.85 | 39 | EDO |
| 4 | 121 | 0.59 | 0.86 | 36 | empty |
| 5 | 99 | 0.57 | 0.86 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1269 Ų buried · 17 hydrogen bonds · protein-protein
- Y–A · 1127 Ų buried · 17 hydrogen bonds · protein-protein
- Z–B · 1071 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6MBK · SETD3, a Histidine Methyltransferase, in Complex with an Actin Peptide and SAH, First… · 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 0.99
- 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 6MBK · PDBe 6MBK · UniProt P60709 · UniProt Q86TU7
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