MolNFT v1 · #149440 · protein + DNA
Structure of two molecules of the chromatin remodelling enzyme CHD1 bound to a nucleosome
6G0L · Histone H3: “Structure of two molecules of the chromatin remodelling enzyme CHD1 bound to a nucleosome”. Electron microscopy, 2 ligands (ADP, BEF), 20 pockets (best druggability 0.88). MolNFT v1 #149440 on GenesisL1: 3D structure…
- PDB
- 6G0L
- Type
- protein + DNA
- Length
- 2,851 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3; Histone H4; Histone H2A type 1; DNA (176-mer); DNA (177-mer); Chromo…
- EC
- 3.6.4.-
- UniProt
- Q92133, P62799, P06897, A0A1L8G0X3, P32657
- Ligands
- ADP, BEF
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 12 distinct chains · 47% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3 | protein | 97 | 66% helix, 2% strand | Q92133 |
| B | Histone H4 | protein | 83 | 61% helix, 5% strand | P62799 |
| C | Histone H2A type 1 | protein | 103 | 54% helix, 4% strand | P06897 |
| D | Histone H4 | protein | 95 | 69% helix, 2% strand | A0A1L8G0X3 |
| E | Histone H3 | protein | 97 | 60% helix, 4% strand | Q92133 |
| F | Histone H4 | protein | 92 | 53% helix, 7% strand | P62799 |
| G | Histone H2A type 1 | protein | 105 | 51% helix, 3% strand | P06897 |
| H | Histone H4 | protein | 93 | 73% helix, 1% strand | A0A1L8G0X3 |
| I | DNA (176-mer) | dna | 176 | — | — |
| J | DNA (177-mer) | dna | 177 | — | — |
| M | Chromo domain-containing protein 1 (EC 3.6.4.-) | protein | 855 | 43% helix, 11% strand | P32657 |
| W | Chromo domain-containing protein 1 (EC 3.6.4.-) | protein | 878 | 39% helix, 10% strand | P32657 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains M, W
- BEF · Beryllium trifluoride ion · ligand · 2 copies · chains M, W
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 | 930 | 0.88 | 0.90 | 87 | empty |
| 2 | 829 | 0.87 | 0.90 | 109 | BEF |
| 3 | 813 | 0.80 | 0.83 | 67 | empty |
| 4 | 147 | 0.80 | 0.96 | 46 | empty |
| 5 | 943 | 0.80 | 0.82 | 97 | ADP, BEF |
Interfaces
45 interfaces between chains.
- I–J · 7717 Ų buried · 567 hydrogen bonds · nucleic-nucleic
- E–F · 2494 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 2419 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 2403 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 2389 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6G0L · Structure of two molecules of the chromatin remodelling enzyme Chd1 bound to a nucleosome · the same entry in another collection · chain W against W, 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 Q92133
- Every structure of UniProt P62799
- Every structure of UniProt P06897
- Every structure of UniProt A0A1L8G0X3
- Every structure of UniProt P32657
- Elsewhere: RCSB PDB 6G0L · PDBe 6G0L · UniProt Q92133 · UniProt P62799 · UniProt P06897 · UniProt A0A1L8G0X3 · UniProt P32657
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