MolNFT v1 · #48615 · protein + DNA
Drosophila nucleosome core
2PYO · DNA (147-mer): “Drosophila nucleosome core”. X-ray diffraction, 2 ligands (MN, CL), 20 pockets (best druggability 0.77). MolNFT v1 #48615 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2PYO
- Type
- protein + DNA
- Length
- 1,067 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (147-mer); Histone H3; Histone H4; Histone H2A; Histone H2B
- UniProt
- P02299, P84040, P84051, P02283
- Ligands
- MN, CL
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 8 distinct chains · 61% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I | DNA (147-mer) | dna | 147 | — | — |
| J | DNA (147-mer) | dna | 147 | — | — |
| A, E | Histone H3 | protein | 99 | 65% helix, 4% strand | P02299 |
| B | Histone H4 | protein | 80 | 61% helix, 8% strand | P84040 |
| C | Histone H2A | protein | 108 | 56% helix, 6% strand | P84051 |
| D, H | Histone H2B | protein | 95 | 73% helix, 4% strand | P02283 |
| F | Histone H4 | protein | 88 | 56% helix, 7% strand | P84040 |
| G | Histone H2A | protein | 109 | 54% helix, 6% strand | P84051 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 14 copies · chains I, J, E, F
- CL · Chloride ion · ion · 4 copies · chains A, J, C, D, 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 679 | 0.77 | 0.82 | 73 | empty |
| 2 | 437 | 0.74 | 0.84 | 49 | empty |
| 3 | 560 | 0.72 | 0.81 | 54 | empty |
| 4 | 814 | 0.72 | 0.78 | 93 | MN |
| 5 | 995 | 0.71 | 0.76 | 75 | empty |
Interfaces
36 interfaces between chains.
- I–J · 6460 Ų buried · 544 hydrogen bonds · nucleic-nucleic
- G–H · 2617 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 2613 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 2605 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 2539 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 2PYO · Drosophila nucleosome core · the same entry in another collection · chain H against H, TM-score 1.00
- P02299 · AlphaFold monomer V2.0 prediction for histone H3 (P02299) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P84051 · AlphaFold monomer V2.0 prediction for histone H2A (P84051) · a predicted model of the same protein · chain C against A, TM-score 0.95
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 P02299
- Every structure of UniProt P84040
- Every structure of UniProt P84051
- Every structure of UniProt P02283
- Elsewhere: RCSB PDB 2PYO · PDBe 2PYO · UniProt P02299 · UniProt P84040 · UniProt P84051 · UniProt P02283
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