Research workbench
Crystal structure of the MLL3-ASH2L-RBBP5 complex
Analyse Crystal structure of the MLL3-ASH2L-RBBP5 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5F6K
- Type
- protein
- Length
- 694 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SET1/ASH2 histone methyltransferase complex subunit ASH2, SET1/ASH2 histone…
- EC
- 2.1.1.43
- UniProt
- Q9UBL3, Q8NEZ4, Q15291
- Ligands
- SAH, ZN
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 7 distinct chains · 9% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SET1/ASH2 histone methyltransferase complex subunit ASH2, SET1/ASH2 histone methyltransferase complex subunit ASH2 | protein | 176 | 2% helix, 47% strand | Q9UBL3 |
| B | SET1/ASH2 histone methyltransferase complex subunit ASH2, SET1/ASH2 histone methyltransferase complex subunit ASH2 | protein | 178 | 2% helix, 47% strand | Q9UBL3 |
| C | Histone-lysine N-methyltransferase 2C (EC 2.1.1.43) | protein | 150 | 19% helix, 38% strand | Q8NEZ4 |
| D | Retinoblastoma-binding protein 5 | protein | 19 | 0% helix, 21% strand | Q15291 |
| E | Histone-lysine N-methyltransferase 2C (EC 2.1.1.43) | protein | 148 | 19% helix, 35% strand | Q8NEZ4 |
| F | Retinoblastoma-binding protein 5 | protein | 17 | 0% helix, 12% strand | Q15291 |
| M | Peptide artkqtark | protein | 6 | 0% helix, 17% strand | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains C, M, E
- ZN · Zinc ion · metal · 2 copies · chains C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 619 | 0.71 | 0.79 | 57 | empty |
| 2 | 443 | 0.67 | 0.79 | 47 | empty |
| 3 | 242 | 0.54 | 0.77 | 43 | empty |
| 4 | 147 | 0.50 | 0.78 | 22 | SAH |
| 5 | 147 | 0.43 | 0.75 | 24 | SAH |
Interfaces
8 interfaces between chains.
- C–D · 794 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 625 Ų buried · 16 hydrogen bonds · protein-protein
- C–M · 590 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 338 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 301 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5F6K · Crystal structure of the MLL3-Ash2L-RbBP5 complex · the same entry in another collection · chain M against M, TM-score 1.00
- Q9UBL3 · AlphaFold monomer V2.0 prediction for SET1/ASH2 histone methyltransferase complex subunit… · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q15291 · AlphaFold monomer V2.0 prediction for retinoblastoma-binding protein 5 (Q15291) · a predicted model of the same protein · chain D against A, TM-score 0.46
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 Q9UBL3
- Every structure of UniProt Q8NEZ4
- Every structure of UniProt Q15291
- Elsewhere: RCSB PDB 5F6K · PDBe 5F6K · UniProt Q9UBL3 · UniProt Q8NEZ4 · UniProt Q15291
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