MolNFT v1 · #118588 · protein
The crystal structure of MLL1 (N3861I/Q3867L) in complex with RBBP5 and ASH2L
5F6L · Retinoblastoma-binding protein 5: “The crystal structure of MLL1 (N3861I/Q3867L) in complex with RBBP5 and ASH2L”. X-ray diffraction, 2 ligands (SAH, ZN), 4 pockets (best druggability 0.49). MolNFT v1 #118588 on GenesisL1: 3D…
- PDB
- 5F6L
- Type
- protein
- Length
- 350 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoblastoma-binding protein 5; SET1/ASH2 histone methyltransferase complex subunit…
- EC
- 2.1.1.43
- UniProt
- Q15291, Q9UBL3, Q03164
- Ligands
- SAH, ZN
- Pockets
- 4 · best druggability 0.49
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| J | Retinoblastoma-binding protein 5 | protein | 19 | 0% helix, 21% strand | Q15291 |
| B | SET1/ASH2 histone methyltransferase complex subunit ASH2 | protein | 178 | 2% helix, 47% strand | Q9UBL3 |
| A | Histone-lysine N-methyltransferase 2A (EC 2.1.1.43) | protein | 153 | 22% helix, 34% strand | Q03164 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 137 | 0.49 | 0.79 | 20 | empty |
| 2 | 177 | 0.47 | 0.76 | 28 | SAH |
| 3 | 83 | 0.38 | 0.77 | 17 | empty |
| 4 | 59 | 0.34 | 0.77 | 13 | empty |
Interfaces
3 interfaces between chains.
- J–A · 849 Ų buried · 16 hydrogen bonds · protein-protein
- J–B · 465 Ų buried · 14 hydrogen bonds · protein-protein
- B–A · 175 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5F6L · The crystal structure of MLL1 (N3861I/Q3867L) in complex with RbBP5 and Ash2L · the same entry in another collection · chain J against J, 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 B 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 J against A, TM-score 0.39
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 Q15291
- Every structure of UniProt Q9UBL3
- Every structure of UniProt Q03164
- Elsewhere: RCSB PDB 5F6L · PDBe 5F6L · UniProt Q15291 · UniProt Q9UBL3 · UniProt Q03164
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