Research workbench
Crystal structure of the nucleosome containing the DNA with tetrahydrofuran (thf)
Analyse Crystal structure of the nucleosome containing the DNA with tetrahydrofuran… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JRG
- Type
- protein + DNA
- Length
- 1,058 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
- Ligands
- MN, CL
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 10 distinct chains · 63% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3.1 | protein | 97 | 65% helix, 4% strand | P68431 |
| B | Histone H4 | protein | 78 | 63% helix, 9% strand | P62805 |
| C | Histone H2A type 1-B/E | protein | 107 | 54% helix, 7% strand | P04908 |
| D | Histone H2B type 1-J | protein | 97 | 71% helix, 4% strand | P06899 |
| E | Histone H3.1 | protein | 99 | 66% helix, 4% strand | P68431 |
| F | Histone H4 | protein | 86 | 58% helix, 8% strand | P62805 |
| G | Histone H2A type 1-B/E | protein | 109 | 54% helix, 6% strand | P04908 |
| H | Histone H2B type 1-J | protein | 96 | 73% helix, 4% strand | P06899 |
| I | DNA (145-mer) | dna | 144 | — | — |
| J | DNA (145-mer) | dna | 145 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 15 copies · chains E, I, J
- CL · Chloride ion · ion · 4 copies · chains A, C, D, J, E, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 752 | 0.79 | 0.83 | 80 | empty |
| 2 | 407 | 0.76 | 0.86 | 54 | empty |
| 3 | 418 | 0.76 | 0.86 | 48 | empty |
| 4 | 641 | 0.67 | 0.77 | 47 | empty |
| 5 | 168 | 0.67 | 0.88 | 31 | empty |
Interfaces
36 interfaces between chains.
- I–J · 6391 Ų buried · 629 hydrogen bonds · nucleic-nucleic
- E–F · 2645 Ų buried · 26 hydrogen bonds · protein-protein
- G–H · 2611 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 2590 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 2533 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 5JRG · Crystal structure of the nucleosome containing the DNA with tetrahydrofuran (THF) · the same entry in another collection · chain A against A, 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 5JRG · PDBe 5JRG · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt P06899
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