MolNFT v1 · #149217 · protein + DNA
Structure of the chromatin remodelling enzyme CHD1 bound to a ubiquitinylated nucleosome
6FTX · Histone H3: “Structure of the chromatin remodelling enzyme CHD1 bound to a ubiquitinylated nucleosome”. Electron microscopy, 2 ligands (BEF, ADP), 20 pockets (best druggability 0.87). MolNFT v1 #149217 on GenesisL1: 3D structure…
- PDB
- 6FTX
- Type
- protein + DNA
- Length
- 2,127 residues
- Chains
- 13
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3; Histone H4; Histone H2A type 1; Histone H2B; Histone H3.3C; DNA (159-mer)…
- UniProt
- S4RAZ3, P62799, P06897, F6TNY0, P02302, P0CG47
- Ligands
- BEF, ADP
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 12 distinct chains · 47% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3 | protein | 97 | 66% helix, 2% strand | S4RAZ3 |
| B | Histone H4 | protein | 83 | 61% helix, 5% strand | P62799 |
| C | Histone H2A type 1 | protein | 103 | 54% helix, 4% strand | P06897 |
| D | Histone H2B | protein | 95 | 69% helix, 2% strand | F6TNY0 |
| E | Histone H3.3C | protein | 110 | 53% helix, 2% strand | P02302 |
| F | Histone H4 | protein | 92 | 53% helix, 4% strand | P62799 |
| G | Histone H2A type 1 | protein | 105 | 51% helix, 3% strand | P06897 |
| H | Histone H2B | protein | 93 | 73% helix, 1% strand | F6TNY0 |
| I | DNA (159-mer) | dna | 159 | — | — |
| J | DNA (160-mer) | dna | 160 | — | — |
| N, O | Polyubiquitin-B | protein | 76 | 14% helix, 22% strand | P0CG47 |
| W | Chromatin-remodeling ATPase | protein | 878 | 39% helix, 10% strand | — |
Ligands and binding sites
- BEF · Beryllium trifluoride ion · ligand · chains W
- ADP · Adenosine-5'-diphosphate · ligand · chains 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 | 668 | 0.87 | 0.91 | 80 | BEF |
| 2 | 287 | 0.82 | 0.93 | 61 | empty |
| 3 | 547 | 0.81 | 0.87 | 50 | empty |
| 4 | 120 | 0.79 | 0.96 | 33 | empty |
| 5 | 504 | 0.74 | 0.83 | 58 | empty |
Interfaces
45 interfaces between chains.
- I–J · 7215 Ų buried · 619 hydrogen bonds · nucleic-nucleic
- E–F · 2485 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 2431 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 2412 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 2389 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6FTX · Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated 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 S4RAZ3
- Every structure of UniProt P62799
- Every structure of UniProt P06897
- Every structure of UniProt F6TNY0
- Every structure of UniProt P02302
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 6FTX · PDBe 6FTX · UniProt S4RAZ3 · UniProt P62799 · UniProt P06897 · UniProt F6TNY0 · UniProt P02302 · UniProt P0CG47
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