MolNFT v1 · #77420 · protein + DNA
2.5 ångström crystal structure of the nucleosome core particle assembled with a 145 bp alpha-satellite DNA (NCP145)
3REH · Histone H3.2: “2.5 ångström crystal structure of the nucleosome core particle assembled with a 145 bp alpha-satellite DNA…”. X-ray diffraction, 2 ligands (MN, SO4), 20 pockets (best druggability 0.81). MolNFT v1 #77420 on GenesisL1…
- PDB
- 3REH
- Type
- protein + DNA
- Length
- 1,055 residues
- Chains
- 10
- 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 (145-mer)
- UniProt
- P84233, P62799, P06897, P02281
- Ligands
- MN, SO4
- 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 |
|---|---|---|---|---|---|
| A, E | Histone H3.2 | protein | 97 | 66% helix, 4% strand | P84233 |
| B | Histone H4 | protein | 82 | 61% helix, 9% strand | P62799 |
| C, G | Histone H2A type 1 | protein | 106 | 57% helix, 7% strand | P06897 |
| D, H | Histone H2B 1.1 | protein | 95 | 74% helix, 4% strand | P02281 |
| F | Histone H4 | protein | 87 | 59% helix, 8% strand | P62799 |
| I | DNA (145-mer) | dna | 145 | — | — |
| J | DNA (145-mer) | dna | 145 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 15 copies · chains E, F, G, H, I, J
- SO4 · Sulfate ion · ion · 3 copies · chains C, D, J, G, H, I
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 | 927 | 0.81 | 0.83 | 92 | empty |
| 2 | 462 | 0.74 | 0.84 | 49 | empty |
| 3 | 302 | 0.73 | 0.86 | 37 | empty |
| 4 | 712 | 0.72 | 0.79 | 58 | SO4 |
| 5 | 706 | 0.70 | 0.78 | 63 | empty |
Interfaces
37 interfaces between chains.
- I–J · 6483 Ų buried · 594 hydrogen bonds · nucleic-nucleic
- C–D · 2659 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 2625 Ų buried · 26 hydrogen bonds · protein-protein
- G–H · 2618 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 2553 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 3REH · 2.5 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 145 bp… · the same entry in another collection · chain I against I, TM-score 1.00
- P84233 · AlphaFold monomer V2.0 prediction for histone H3.2 (P84233) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P06897 · AlphaFold monomer V2.0 prediction for histone H2A type 1 (P06897) · a predicted model of the same protein · chain C against A, TM-score 0.96
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
- Elsewhere: RCSB PDB 3REH · PDBe 3REH · UniProt P84233 · UniProt P62799 · UniProt P06897 · UniProt P02281
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