MolNFT v1 · #160872 · protein + DNA
Cryo-EM structure of MLL1 core complex bound to the nucleosome
6PWV · Retinoblastoma-binding protein 5: “Cryo-EM structure of MLL1 core complex bound to the nucleosome”. Electron microscopy, 2 ligands (SAH, ZN), 20 pockets (best druggability 0.81). MolNFT v1 #160872 on GenesisL1: 3D structure, binding…
- PDB
- 6PWV
- Type
- protein + DNA
- Length
- 2,295 residues
- Chains
- 16
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoblastoma-binding protein 5; Wd repeat-containing protein 5; Histone-lysine…
- EC
- 2.1.1.43
- UniProt
- Q15291, P61964, Q03164, P84233, P62799, P06897, P02281, Q9C005, Q9UBL3
- Ligands
- SAH, ZN
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 12 distinct chains · 23% helix, 29% 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 2.1.1.43) | protein | 153 | 22% helix, 37% strand | Q03164 |
| G, K | Histone H3.2 | protein | 98 | 66% helix, 2% strand | P84233 |
| H, L | Histone H4 | protein | 82 | 57% helix, 4% 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, 2% strand | P02281 |
| O | DNA (147-mer) | dna | 146 | — | — |
| P | DNA (147-mer) | dna | 146 | — | — |
| E | Protein dpy-30 homolog | protein | 47 | 70% helix, 0% strand | Q9C005 |
| F | Protein dpy-30 homolog | protein | 50 | 68% helix, 0% strand | Q9C005 |
| D | SET1/ASH2 histone methyltransferase complex subunit ASH2 | protein | 357 | 10% helix, 27% strand | Q9UBL3 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains C
- ZN · Zinc ion · metal · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 898 | 0.81 | 0.83 | 64 | empty |
| 2 | 359 | 0.81 | 0.90 | 57 | empty |
| 3 | 680 | 0.81 | 0.85 | 80 | empty |
| 4 | 720 | 0.80 | 0.84 | 66 | empty |
| 5 | 539 | 0.78 | 0.85 | 77 | empty |
Interfaces
51 interfaces between chains.
- O–P · 6512 Ų buried · 738 hydrogen bonds · nucleic-nucleic
- M–N · 2454 Ų buried · 32 hydrogen bonds · protein-protein
- I–J · 2325 Ų buried · 24 hydrogen bonds · protein-protein
- G–H · 2302 Ų buried · 28 hydrogen bonds · protein-protein
- K–L · 2282 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 6PWV · Cryo-EM structure of MLL1 core complex bound to the nucleosome · the same entry in another collection · chain N against N, 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 P84233
- Every structure of UniProt P62799
- Every structure of UniProt P06897
- Every structure of UniProt P02281
- Every structure of UniProt Q9C005
- Every structure of UniProt Q9UBL3
- Elsewhere: RCSB PDB 6PWV · PDBe 6PWV · UniProt Q15291 · UniProt P61964 · UniProt Q03164 · UniProt P84233 · UniProt P62799 · UniProt P06897 · UniProt P02281 · UniProt Q9C005 · UniProt Q9UBL3
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