Research workbench
Telomeric trinucleosome in open state
Analyse Telomeric trinucleosome 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
- 7V9S
- Type
- protein + DNA
- Length
- 3,156 residues
- Chains
- 26
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.1; Histone H4; Histone H2A type 1-B/E; Histone H2B type 1-K; DNA (408-mer)
- UniProt
- P68431, P62805, P04908, O60814
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 12 distinct chains · 58% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, K, O, S, W | Histone H3.1 | protein | 100 | 61% helix, 3% strand | P68431 |
| B, P | Histone H4 | protein | 84 | 61% helix, 7% strand | P62805 |
| C, U, Y | Histone H2A type 1-B/E | protein | 109 | 53% helix, 6% strand | P04908 |
| D, N, V | Histone H2B type 1-K | protein | 99 | 69% helix, 4% strand | O60814 |
| F, L | Histone H4 | protein | 87 | 59% helix, 5% strand | P62805 |
| G | Histone H2A type 1-B/E | protein | 120 | 48% helix, 4% strand | P04908 |
| H, R, Z | Histone H2B type 1-K | protein | 98 | 70% helix, 2% strand | O60814 |
| M | Histone H2A type 1-B/E | protein | 119 | 49% helix, 4% strand | P04908 |
| Q | Histone H2A type 1-B/E | protein | 110 | 53% helix, 6% strand | P04908 |
| T, X | Histone H4 | protein | 83 | 63% helix, 6% strand | P62805 |
| I | DNA (408-mer) | dna | 388 | — | — |
| J | DNA (408-mer) | dna | 393 | — | — |
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 | 982 | 0.79 | 0.81 | 80 | empty |
| 2 | 882 | 0.79 | 0.81 | 75 | empty |
| 3 | 888 | 0.78 | 0.81 | 84 | empty |
| 4 | 457 | 0.76 | 0.85 | 55 | empty |
| 5 | 580 | 0.75 | 0.82 | 50 | empty |
Interfaces
107 interfaces between chains.
- I–J · 17818 Ų buried · 1,853 hydrogen bonds · nucleic-nucleic
- O–P · 2645 Ų buried · 23 hydrogen bonds · protein-protein
- K–L · 2626 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 2602 Ų buried · 20 hydrogen bonds · protein-protein
- W–X · 2591 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- P68431 · AlphaFold monomer V2.0 prediction for histone H3.1 (P68431) · a predicted model of the same protein · chain A against A, TM-score 0.95
- P62805 · AlphaFold monomer V2.0 prediction for histone H4 (P62805) · a predicted model of the same protein · chain X against A, TM-score 0.93
- P04908 · AlphaFold monomer V2.0 prediction for histone H2A type 1-B/E (P04908) · a predicted model of the same protein · chain Y against A, TM-score 0.92
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 7V9S · PDBe 7V9S · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt O60814
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