MolNFT v1 · #181945 · protein + DNA
Cryo-EM structure of MLL1-ncp (H3K4M) complex, MODE02
7MBN · Retinoblastoma-binding protein 5: “Cryo-EM structure of MLL1-ncp (H3K4M) complex, MODE02”. Electron microscopy, 20 pockets (best druggability 0.81). MolNFT v1 #181945 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7MBN
- Type
- protein + DNA
- Length
- 2,098 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 · 10 distinct chains · 22% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoblastoma-binding protein 5 | protein | 333 | 2% helix, 47% strand | Q15291 |
| B | Wd repeat-containing protein 5 | protein | 303 | 0% helix, 52% strand | P61964 |
| C | Histone-lysine N-methyltransferase 2A (EC 2.1.1.354) | protein | 153 | 22% helix, 37% strand | Q03164 |
| D | SET1/ASH2 histone methyltransferase complex subunit ASH2 | protein | 257 | 12% helix, 34% strand | Q9UBL3 |
| G, K | Histone H3 | protein | 98 | 66% helix, 2% strand | A0A310TTQ1 |
| H, L | Histone H4 | protein | 82 | 57% helix, 4% strand | P62799 |
| I, M | Histone H2A | protein | 107 | 55% helix, 2% strand | Q6AZJ8 |
| J, N | Histone H2B 1.1 | protein | 93 | 73% helix, 2% strand | P02281 |
| O | DNA (146-mer) | dna | 146 | — | — |
| P | DNA (146-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 | 904 | 0.81 | 0.83 | 64 | empty |
| 2 | 1002 | 0.79 | 0.81 | 75 | empty |
| 3 | 119 | 0.79 | 0.97 | 28 | empty |
| 4 | 557 | 0.78 | 0.85 | 81 | empty |
| 5 | 161 | 0.77 | 0.93 | 32 | empty |
Interfaces
46 interfaces between chains.
- O–P · 6497 Ų buried · 760 hydrogen bonds · nucleic-nucleic
- M–N · 2433 Ų buried · 28 hydrogen bonds · protein-protein
- K–L · 2336 Ų buried · 24 hydrogen bonds · protein-protein
- G–H · 2318 Ų buried · 30 hydrogen bonds · protein-protein
- I–J · 2308 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 7MBN · Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode02 · the same entry in another collection · chain O against O, 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 7MBN · PDBe 7MBN · UniProt Q15291 · UniProt P61964 · UniProt Q03164 · UniProt Q9UBL3 · UniProt A0A310TTQ1 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281
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