MolNFT v1 · #168108 · protein + DNA
Cryo-EM structure of MLL1 in complex with RBBP5, WDR5, SET1, and ASH2L bound to the nucleosome (CLASS02)
6W5M · Retinoblastoma-binding protein 5: “Cryo-EM structure of MLL1 in complex with RBBP5, WDR5, SET1, and ASH2L bound to the nucleosome (CLASS02)”. Electron microscopy, 20 pockets (best druggability 0.85). MolNFT v1 #168108 on GenesisL1…
- PDB
- 6W5M
- Type
- protein + DNA
- Length
- 2,021 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoblastoma-binding protein 5; Wd repeat-containing protein 5; Histone-lysine…
- EC
- 2.1.1.354
- UniProt
- Q15291, P61964, Q03164, Q9UBL3, P84233, P62799, P06897, P02281
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 10 distinct chains · 23% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoblastoma-binding protein 5 | protein | 306 | 2% helix, 50% strand | Q15291 |
| B | Wd repeat-containing protein 5 | protein | 298 | 0% helix, 52% strand | P61964 |
| C | Histone-lysine N-methyltransferase 2A (EC 2.1.1.354) | protein | 148 | 22% helix, 38% strand | Q03164 |
| D | SET1/ASH2 histone methyltransferase complex subunit ASH2 | protein | 217 | 12% helix, 35% strand | Q9UBL3 |
| G, K | Histone H3.2 | protein | 98 | 66% helix, 3% strand | P84233 |
| H, L | Histone H4 | protein | 82 | 57% helix, 5% strand | P62799 |
| I, M | Histone H2A type 1 | protein | 107 | 55% helix, 4% strand | P06897 |
| J, N | Histone H2B 1.1 | protein | 93 | 73% helix, 4% strand | P02281 |
| O | DNA (147-mer) | dna | 146 | — | — |
| P | DNA (147-mer) | dna | 146 | — | — |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 668 | 0.85 | 0.89 | 86 | empty |
| 2 | 811 | 0.85 | 0.88 | 122 | empty |
| 3 | 907 | 0.82 | 0.84 | 61 | empty |
| 4 | 262 | 0.79 | 0.91 | 47 | empty |
| 5 | 682 | 0.76 | 0.81 | 59 | empty |
Interfaces
44 interfaces between chains.
- O–P · 6483 Ų buried · 795 hydrogen bonds · nucleic-nucleic
- M–N · 2417 Ų buried · 29 hydrogen bonds · protein-protein
- I–J · 2313 Ų buried · 17 hydrogen bonds · protein-protein
- G–H · 2292 Ų buried · 29 hydrogen bonds · protein-protein
- K–L · 2289 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 6W5M · Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the… · the same entry in another collection · chain P against P, TM-score 1.00
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 P61964
- Every structure of UniProt Q03164
- Every structure of UniProt Q9UBL3
- Every structure of UniProt P84233
- Every structure of UniProt P62799
- Every structure of UniProt P06897
- Every structure of UniProt P02281
- Elsewhere: RCSB PDB 6W5M · PDBe 6W5M · UniProt Q15291 · UniProt P61964 · UniProt Q03164 · UniProt Q9UBL3 · UniProt P84233 · UniProt P62799 · UniProt P06897 · UniProt P02281
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