Research workbench
Nucleosome stack of the 4X177 nucleosome array containing H1
Analyse Nucleosome stack of the 4X177 nucleosome array containing H1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PEV
- Type
- protein + DNA
- Length
- 2,230 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.2; Histone H4; Histone H2A type 1-B/E; Histone H2B type 1-K; DNA (520-mer)
- UniProt
- Q71DI3, P62805, P04908, O60814
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 6 distinct chains · 62% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, K, O | Histone H3.2 | protein | 97 | 68% helix, 4% strand | Q71DI3 |
| B, F, L, P | Histone H4 | protein | 83 | 55% helix, 7% strand | P62805 |
| C, G, M, Q | Histone H2A type 1-B/E | protein | 109 | 54% helix, 6% strand | P04908 |
| D, H, N, R | Histone H2B type 1-K | protein | 95 | 72% helix, 4% strand | O60814 |
| J | DNA (520-mer) | dna | 347 | — | — |
| I | DNA (520-mer) | dna | 347 | — | — |
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 | 872 | 0.79 | 0.82 | 75 | empty |
| 2 | 486 | 0.79 | 0.86 | 58 | empty |
| 3 | 392 | 0.78 | 0.88 | 48 | empty |
| 4 | 124 | 0.78 | 0.96 | 41 | empty |
| 5 | 401 | 0.77 | 0.87 | 55 | empty |
Interfaces
75 interfaces between chains.
- J–I · 15747 Ų buried · 1,485 hydrogen bonds · nucleic-nucleic
- M–N · 2603 Ų buried · 23 hydrogen bonds · protein-protein
- G–H · 2540 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 2528 Ų buried · 26 hydrogen bonds · protein-protein
- K–L · 2525 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 7PEV · Nucleosome stack of the 4x177 nucleosome array containing H1 · the same entry in another collection · chain K against K, 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 Q71DI3
- Every structure of UniProt P62805
- Every structure of UniProt P04908
- Every structure of UniProt O60814
- Elsewhere: RCSB PDB 7PEV · PDBe 7PEV · UniProt Q71DI3 · UniProt P62805 · UniProt P04908 · UniProt O60814
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