Research workbench
Nucleosome and GAL4 complex
Analyse Nucleosome and GAL4 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K7G
- Type
- protein + DNA
- Length
- 1,012 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3; Histone H4; Histone H2A.1; Histone H2B.1; DNA (147-mer); Centromere…
- UniProt
- P61830, P02309, P04911, P02293, P40969
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.75
Structure
electron microscopy · 8 distinct chains · 56% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Histone H3 | protein | 91 | 56% helix, 4% strand | P61830 |
| B, F | Histone H4 | protein | 80 | 66% helix, 8% strand | P02309 |
| C | Histone H2A.1 | protein | 97 | 55% helix, 5% strand | P04911 |
| D, H | Histone H2B.1 | protein | 92 | 74% helix, 4% strand | P02293 |
| G | Histone H2A.1 | protein | 100 | 49% helix, 4% strand | P04911 |
| I | DNA (147-mer) | dna | 123 | — | — |
| J | DNA (147-mer) | dna | 123 | — | — |
| M | Centromere DNA-binding protein complex CBF3 subunit B | protein | 43 | 21% helix, 0% strand | P40969 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 468 | 0.75 | 0.84 | 59 | empty |
| 2 | 518 | 0.75 | 0.83 | 62 | empty |
| 3 | 449 | 0.75 | 0.84 | 57 | empty |
| 4 | 52 | 0.71 | 0.98 | 16 | empty |
| 5 | 788 | 0.71 | 0.77 | 57 | empty |
Interfaces
39 interfaces between chains.
- I–J · 5827 Ų buried · 559 hydrogen bonds · nucleic-nucleic
- C–D · 2628 Ų buried · 22 hydrogen bonds · protein-protein
- G–H · 2505 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 2352 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 2319 Ų buried · 10 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 P61830
- Every structure of UniProt P02309
- Every structure of UniProt P04911
- Every structure of UniProt P02293
- Every structure of UniProt P40969
- Elsewhere: RCSB PDB 7K7G · PDBe 7K7G · UniProt P61830 · UniProt P02309 · UniProt P04911 · UniProt P02293 · UniProt P40969
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