Research workbench
The structure of ALC1 bound to the nucleosome
Analyse The structure of ALC1 bound to the nucleosome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ENN
- Type
- protein + DNA
- Length
- 1,592 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chromodomain-helicase-DNA-binding protein 1-like; Histone H3.2; Histone H4; Histone H2A…
- EC
- 3.6.4.12
- UniProt
- Q86WJ1, P84233, P62799, P06897, P02281
- Ligands
- ADP, BEF
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 9 distinct chains · 53% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| K | Chromodomain-helicase-DNA-binding protein 1-like (EC 3.6.4.12) | protein | 539 | 44% helix, 12% strand | Q86WJ1 |
| A | Histone H3.2 | protein | 98 | 64% helix, 4% strand | P84233 |
| L | Histone H4 | protein | 88 | 57% helix, 8% strand | P62799 |
| C, G | Histone H2A type 1 | protein | 107 | 53% helix, 7% strand | P06897 |
| D, H | Histone H2B 1.1 | protein | 93 | 74% helix, 4% strand | P02281 |
| E | Histone H3.2 | protein | 95 | 66% helix, 4% strand | P84233 |
| F | Histone H4 | protein | 80 | 61% helix, 9% strand | P62799 |
| I | DNA (167-mer) | dna | 146 | — | — |
| J | DNA (167-mer) | dna | 146 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains K
- BEF · Beryllium trifluoride ion · ligand · chains K
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 | 995 | 0.78 | 0.80 | 88 | empty |
| 2 | 674 | 0.78 | 0.83 | 68 | empty |
| 3 | 202 | 0.78 | 0.93 | 26 | empty |
| 4 | 447 | 0.75 | 0.85 | 47 | empty |
| 5 | 1132 | 0.74 | 0.77 | 69 | empty |
Interfaces
39 interfaces between chains.
- I–J · 6679 Ų buried · 483 hydrogen bonds · nucleic-nucleic
- G–H · 2595 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 2584 Ų buried · 22 hydrogen bonds · protein-protein
- A–L · 2536 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 2507 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
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 Q86WJ1
- Every structure of UniProt P84233
- Every structure of UniProt P62799
- Every structure of UniProt P06897
- Every structure of UniProt P02281
- Elsewhere: RCSB PDB 7ENN · PDBe 7ENN · UniProt Q86WJ1 · UniProt P84233 · UniProt P62799 · UniProt P06897 · UniProt P02281
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