Research workbench
Crystal structure of a 197-bp palindromic 601L nucleosome in complex with linker histone H1
Analyse Crystal structure of a 197-bp palindromic 601L nucleosome in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NL0
- Type
- protein + DNA
- Length
- 1,793 residues
- Chains
- 17
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.2; Histone H4; Histone H2A type 1; Histone H2B 1.1; DNA (197-mer); Histone…
- UniProt
- P84233, P62799, P06897, P02281, P22844
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 12 distinct chains · 63% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, K | Histone H3.2 | protein | 98 | 65% helix, 4% strand | P84233 |
| B, F, L | Histone H4 | protein | 83 | 59% helix, 8% strand | P62799 |
| C, M | Histone H2A type 1 | protein | 105 | 56% helix, 7% strand | P06897 |
| D, N | Histone H2B 1.1 | protein | 95 | 74% helix, 4% strand | P02281 |
| E | Histone H3.2 | protein | 97 | 66% helix, 4% strand | P84233 |
| G | Histone H2A type 1 | protein | 103 | 59% helix, 7% strand | P06897 |
| H | Histone H2B 1.1 | protein | 96 | 73% helix, 4% strand | P02281 |
| I | DNA (197-mer) | dna | 193 | — | — |
| J | DNA (197-mer) | dna | 193 | — | — |
| S | DNA (197-mer) | dna | 96 | — | — |
| T | DNA (197-mer) | dna | 97 | — | — |
| Z | Histone H1.0-B | protein | 73 | 51% helix, 18% strand | P22844 |
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 | 781 | 0.80 | 0.84 | 79 | empty |
| 2 | 557 | 0.79 | 0.85 | 71 | empty |
| 3 | 415 | 0.78 | 0.87 | 48 | empty |
| 4 | 1171 | 0.72 | 0.76 | 102 | empty |
| 5 | 984 | 0.71 | 0.76 | 71 | empty |
Interfaces
53 interfaces between chains.
- I–J · 8854 Ų buried · 827 hydrogen bonds · nucleic-nucleic
- S–T · 4373 Ų buried · 403 hydrogen bonds · nucleic-nucleic
- G–H · 2725 Ų buried · 29 hydrogen bonds · protein-protein
- M–N · 2634 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 2616 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 5NL0 · Crystal structure of a 197-bp palindromic 601L nucleosome in complex with linker histone… · the same entry in another collection · chain Z against Z, 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 P84233
- Every structure of UniProt P62799
- Every structure of UniProt P06897
- Every structure of UniProt P02281
- Every structure of UniProt P22844
- Elsewhere: RCSB PDB 5NL0 · PDBe 5NL0 · UniProt P84233 · UniProt P62799 · UniProt P06897 · UniProt P02281 · UniProt P22844
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