Research workbench
Nucleosome 2 of the 4X177 nucleosome array containing H1
Analyse Nucleosome 2 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
- 7PEX
- Type
- protein + DNA
- Length
- 1,197 residues
- Chains
- 11
- 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 (177-mer)…
- UniProt
- Q71DI3, P62805, P04908, O60814, P10412
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 7 distinct chains · 60% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| a, e | Histone H3.2 | protein | 97 | 67% helix, 3% strand | Q71DI3 |
| b, f | Histone H4 | protein | 83 | 60% helix, 7% strand | P62805 |
| c, g | Histone H2A type 1-B/E | protein | 109 | 50% helix, 6% strand | P04908 |
| d, h | Histone H2B type 1-K | protein | 95 | 73% helix, 4% strand | O60814 |
| J | DNA (177-mer) | dna | 177 | — | — |
| I | DNA (177-mer) | dna | 177 | — | — |
| u | Histone H1.4 | protein | 75 | 49% helix, 12% strand | P10412 |
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 | 1095 | 0.82 | 0.83 | 98 | empty |
| 2 | 252 | 0.74 | 0.89 | 40 | empty |
| 3 | 359 | 0.73 | 0.85 | 40 | empty |
| 4 | 384 | 0.73 | 0.85 | 42 | empty |
| 5 | 327 | 0.72 | 0.85 | 36 | empty |
Interfaces
39 interfaces between chains.
- J–I · 7958 Ų buried · 688 hydrogen bonds · nucleic-nucleic
- c–d · 2610 Ų buried · 29 hydrogen bonds · protein-protein
- g–h · 2580 Ų buried · 19 hydrogen bonds · protein-protein
- e–f · 2537 Ų buried · 15 hydrogen bonds · protein-protein
- a–b · 2493 Ų buried · 17 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 Q71DI3
- Every structure of UniProt P62805
- Every structure of UniProt P04908
- Every structure of UniProt O60814
- Every structure of UniProt P10412
- Elsewhere: RCSB PDB 7PEX · PDBe 7PEX · UniProt Q71DI3 · UniProt P62805 · UniProt P04908 · UniProt O60814 · UniProt P10412
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