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The crystal structure of the nucleosome containing cyclobutane pyrimidine dimer
Analyse The crystal structure of the nucleosome containing cyclobutane pyrimidine dimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5B24
- Type
- protein + DNA
- Length
- 1,045 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.1; Histone H4; Histone H2A type 1-B/E; Histone H2B type 1-J; DNA (145-mer)
- UniProt
- P68431, P62805, P04908, P06899
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 9 distinct chains · 63% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3.1 | protein | 97 | 64% helix, 4% strand | P68431 |
| B | Histone H4 | protein | 78 | 63% helix, 9% strand | P62805 |
| C | Histone H2A type 1-B/E | protein | 108 | 51% helix, 6% strand | P04908 |
| D | Histone H2B type 1-J | protein | 93 | 75% helix, 4% strand | P06899 |
| E | Histone H3.1 | protein | 99 | 65% helix, 4% strand | P68431 |
| F | Histone H4 | protein | 84 | 60% helix, 8% strand | P62805 |
| G | Histone H2A type 1-B/E | protein | 104 | 53% helix, 7% strand | P04908 |
| H | Histone H2B type 1-J | protein | 92 | 75% helix, 4% strand | P06899 |
| I, J | DNA (145-mer) | dna | 145 | — | — |
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 | 831 | 0.80 | 0.83 | 70 | empty |
| 2 | 397 | 0.77 | 0.87 | 46 | empty |
| 3 | 387 | 0.76 | 0.86 | 46 | empty |
| 4 | 208 | 0.70 | 0.87 | 31 | empty |
| 5 | 659 | 0.69 | 0.77 | 58 | empty |
Interfaces
36 interfaces between chains.
- I–J · 6359 Ų buried · 537 hydrogen bonds · nucleic-nucleic
- E–F · 2705 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 2671 Ų buried · 30 hydrogen bonds · protein-protein
- G–H · 2590 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2550 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 5B24 · The crystal structure of the nucleosome containing cyclobutane pyrimidine dimer · the same entry in another collection · chain F against F, 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 P06899
- Elsewhere: RCSB PDB 5B24 · PDBe 5B24 · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt P06899
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