Research workbench
Cryo-EM structure of MLL1-ncp (H3K4M) complex, MODE01
Analyse Cryo-EM structure of MLL1-ncp (H3K4M) complex, MODE01 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MBM
- Type
- protein + DNA
- Length
- 2,037 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, A0A310TTQ1, P62799, Q6AZJ8, P02281
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 13 distinct chains · 26% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoblastoma-binding protein 5 | protein | 339 | 1% helix, 32% strand | Q15291 |
| B | Wd repeat-containing protein 5 | protein | 300 | 0% helix, 39% strand | P61964 |
| C | Histone-lysine N-methyltransferase 2A (EC 2.1.1.354) | protein | 179 | 15% helix, 17% strand | Q03164 |
| D | SET1/ASH2 histone methyltransferase complex subunit ASH2 | protein | 176 | 2% helix, 24% strand | Q9UBL3 |
| G, K | Histone H3 | protein | 97 | 65% helix, 2% strand | A0A310TTQ1 |
| H | Histone H4 | protein | 80 | 59% helix, 6% strand | P62799 |
| I | Histone H2A | protein | 107 | 46% helix, 2% strand | Q6AZJ8 |
| J | Histone H2B 1.1 | protein | 94 | 72% helix, 2% strand | P02281 |
| L | Histone H4 | protein | 78 | 65% helix, 3% strand | P62799 |
| M | Histone H2A | protein | 105 | 50% helix, 7% strand | Q6AZJ8 |
| N | Histone H2B 1.1 | protein | 95 | 73% helix, 4% strand | P02281 |
| O | DNA (145-mer) | dna | 145 | — | — |
| P | DNA (145-mer) | dna | 145 | — | — |
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 | 958 | 0.81 | 0.83 | 67 | empty |
| 2 | 233 | 0.80 | 0.92 | 45 | empty |
| 3 | 1041 | 0.79 | 0.80 | 91 | empty |
| 4 | 586 | 0.76 | 0.83 | 58 | empty |
| 5 | 380 | 0.75 | 0.86 | 49 | empty |
Interfaces
51 interfaces between chains.
- O–P · 6704 Ų buried · 572 hydrogen bonds · nucleic-nucleic
- I–J · 2600 Ų buried · 9 hydrogen bonds · protein-protein
- M–N · 2577 Ų buried · 7 hydrogen bonds · protein-protein
- K–L · 2457 Ų buried · 7 hydrogen bonds · protein-protein
- G–H · 2436 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7MBM · Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode01 · 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 A0A310TTQ1
- Every structure of UniProt P62799
- Every structure of UniProt Q6AZJ8
- Every structure of UniProt P02281
- Elsewhere: RCSB PDB 7MBM · PDBe 7MBM · UniProt Q15291 · UniProt P61964 · UniProt Q03164 · UniProt Q9UBL3 · UniProt A0A310TTQ1 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281
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