Research workbench
Structure of the marseillevirus nucleosome
Analyse Structure of the marseillevirus nucleosome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LV8
- Type
- protein + DNA
- Length
- 1,006 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone doublet delta-gamma (delta); Histone doublet delta-gamma (gamma); Histone doublet…
- UniProt
- D2XB48, A0A2R3ZQX0, D2XB49
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 6 distinct chains · 59% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, F | Histone doublet delta-gamma (delta) | protein | 97 | 46% helix, 4% strand | D2XB48 |
| A, E | Histone doublet delta-gamma (gamma) | protein | 102 | 57% helix, 3% strand | D2XB48 |
| D, H | Histone doublet beta-alpha (beta) | protein | 89 | 74% helix, 4% strand | A0A2R3ZQX0 |
| C, G | Histone doublet beta-alpha (alpha) | protein | 94 | 62% helix, 5% strand | D2XB49 |
| I | DNA (123-mer) | dna | 121 | — | — |
| J | DNA (123-mer) | dna | 121 | — | — |
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 | 749 | 0.78 | 0.82 | 56 | empty |
| 2 | 649 | 0.76 | 0.82 | 47 | empty |
| 3 | 355 | 0.76 | 0.87 | 52 | empty |
| 4 | 609 | 0.72 | 0.80 | 52 | empty |
| 5 | 425 | 0.69 | 0.81 | 44 | empty |
Interfaces
35 interfaces between chains.
- I–J · 5437 Ų buried · 420 hydrogen bonds · nucleic-nucleic
- B–A · 2916 Ų buried · 21 hydrogen bonds · protein-protein
- F–E · 2901 Ų buried · 19 hydrogen bonds · protein-protein
- D–C · 2607 Ų buried · 21 hydrogen bonds · protein-protein
- H–G · 2546 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 7LV8 · Structure of the Marseillevirus nucleosome · the same entry in another collection · chain B against B, 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 D2XB48
- Every structure of UniProt A0A2R3ZQX0
- Every structure of UniProt D2XB49
- Elsewhere: RCSB PDB 7LV8 · PDBe 7LV8 · UniProt D2XB48 · UniProt A0A2R3ZQX0 · UniProt D2XB49
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