Research workbench
Telomeric dinucleosome in open state
Analyse Telomeric dinucleosome in open state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7V9C
- Type
- protein + DNA
- Length
- 2,064 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (275-mer); Histone H3.1; Histone H4; Histone H2A type 1-B/E; Histone H2B type 1-K
- UniProt
- P68431, P62805, P04908, O60814
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 10 distinct chains · 62% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I | DNA (275-mer) | dna | 273 | — | — |
| J | DNA (275-mer) | dna | 273 | — | — |
| A, K | Histone H3.1 | protein | 95 | 64% helix, 1% strand | P68431 |
| B, L | Histone H4 | protein | 82 | 62% helix, 5% strand | P62805 |
| C, M | Histone H2A type 1-B/E | protein | 114 | 49% helix, 4% strand | P04908 |
| D, N | Histone H2B type 1-K | protein | 95 | 72% helix, 2% strand | O60814 |
| E, O | Histone H3.1 | protein | 96 | 64% helix, 1% strand | P68431 |
| F, P | Histone H4 | protein | 78 | 65% helix, 5% strand | P62805 |
| G, Q | Histone H2A type 1-B/E | protein | 105 | 53% helix, 5% strand | P04908 |
| H, R | Histone H2B type 1-K | protein | 94 | 72% helix, 2% strand | O60814 |
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 | 1191 | 0.80 | 0.81 | 109 | empty |
| 2 | 1101 | 0.80 | 0.81 | 86 | empty |
| 3 | 605 | 0.78 | 0.84 | 60 | empty |
| 4 | 579 | 0.77 | 0.84 | 58 | empty |
| 5 | 653 | 0.77 | 0.83 | 64 | empty |
Interfaces
69 interfaces between chains.
- I–J · 10494 Ų buried · 453 hydrogen bonds · nucleic-nucleic
- K–L · 2663 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 2662 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 2626 Ų buried · 23 hydrogen bonds · protein-protein
- M–N · 2625 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 7V9C · Telomeric Dinucleosome in open state · the same entry in another collection · chain H against H, 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 P68431
- Every structure of UniProt P62805
- Every structure of UniProt P04908
- Every structure of UniProt O60814
- Elsewhere: RCSB PDB 7V9C · PDBe 7V9C · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt O60814
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