MolNFT v1 · #129069 · protein + DNA
Structure of nucleosome-CHD1 complex
5O9G · Histone H3.2: “Structure of nucleosome-CHD1 complex”. Electron microscopy, 2 ligands (ADP, BEF), 20 pockets (best druggability 0.87). MolNFT v1 #129069 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5O9G
- Type
- protein + DNA
- Length
- 1,934 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.2; Histone H4; Histone H2A; Histone H2B 1.1; DNA (162-mer); Chromo…
- EC
- 3.6.4.-
- UniProt
- P84233, P62799, Q6AZJ8, P02281, P32657
- Ligands
- ADP, BEF
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 11 distinct chains · 52% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3.2 | protein | 97 | 67% helix, 0% strand | P84233 |
| B | Histone H4 | protein | 87 | 56% helix, 2% strand | P62799 |
| C | Histone H2A | protein | 103 | 54% helix, 4% strand | Q6AZJ8 |
| D | Histone H2B 1.1 | protein | 95 | 67% helix, 2% strand | P02281 |
| E | Histone H3.2 | protein | 97 | 66% helix, 1% strand | P84233 |
| F | Histone H4 | protein | 78 | 63% helix, 4% strand | P62799 |
| G | Histone H2A | protein | 105 | 55% helix, 5% strand | Q6AZJ8 |
| H | Histone H2B 1.1 | protein | 93 | 70% helix, 3% strand | P02281 |
| I | DNA (162-mer) | dna | 162 | — | — |
| J | DNA (162-mer) | dna | 162 | — | — |
| W | Chromo domain-containing protein 1 (EC 3.6.4.-) | protein | 855 | 43% helix, 11% strand | P32657 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains W
- BEF · Beryllium trifluoride ion · 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 | 804 | 0.87 | 0.90 | 75 | empty |
| 2 | 566 | 0.82 | 0.88 | 69 | empty |
| 3 | 974 | 0.80 | 0.82 | 97 | ADP, BEF |
| 4 | 899 | 0.78 | 0.81 | 72 | empty |
| 5 | 333 | 0.78 | 0.89 | 52 | empty |
Interfaces
40 interfaces between chains.
- I–J · 7300 Ų buried · 581 hydrogen bonds · nucleic-nucleic
- A–B · 2603 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 2570 Ų buried · 12 hydrogen bonds · protein-protein
- G–H · 2539 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 2420 Ų buried · 14 hydrogen bonds · protein-protein
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 P84233
- Every structure of UniProt P62799
- Every structure of UniProt Q6AZJ8
- Every structure of UniProt P02281
- Every structure of UniProt P32657
- Elsewhere: RCSB PDB 5O9G · PDBe 5O9G · UniProt P84233 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281 · UniProt P32657
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