MolNFT v1 · #46269 · protein + DNA
Nucleosome core particle containing 145 bp of DNA
2NZD · DNA (145-mer): “Nucleosome core particle containing 145 bp of DNA”. X-ray diffraction, 1 ligand (MN), 20 pockets (best druggability 0.81). MolNFT v1 #46269 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2NZD
- Type
- protein + DNA
- Length
- 1,055 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (145-mer); Histone H3; Histone H4; Histone H2A; Histone H2B
- UniProt
- P62799, Q6AZJ8, P02281
- Ligands
- MN
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 7 distinct chains · 63% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I | DNA (145-mer) | dna | 145 | — | — |
| J | DNA (145-mer) | dna | 145 | — | — |
| A, E | Histone H3 | protein | 97 | 66% helix, 4% strand | — |
| B | Histone H4 | protein | 82 | 61% helix, 9% strand | P62799 |
| C, G | Histone H2A | protein | 106 | 55% helix, 7% strand | Q6AZJ8 |
| D, H | Histone H2B | protein | 95 | 73% helix, 4% strand | P02281 |
| F | Histone H4 | protein | 87 | 59% helix, 8% strand | P62799 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 11 copies · chains I, J, E, F
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 | 892 | 0.81 | 0.83 | 83 | empty |
| 2 | 338 | 0.74 | 0.86 | 46 | empty |
| 3 | 335 | 0.73 | 0.86 | 40 | empty |
| 4 | 889 | 0.73 | 0.78 | 94 | empty |
| 5 | 382 | 0.65 | 0.79 | 22 | empty |
Interfaces
37 interfaces between chains.
- I–J · 6427 Ų buried · 599 hydrogen bonds · nucleic-nucleic
- C–D · 2668 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 2634 Ų buried · 26 hydrogen bonds · protein-protein
- G–H · 2624 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 2551 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 2NZD · Nucleosome core particle containing 145 bp of DNA · the same entry in another collection · chain I against I, 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 P62799
- Every structure of UniProt Q6AZJ8
- Every structure of UniProt P02281
- Elsewhere: RCSB PDB 2NZD · PDBe 2NZD · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281
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