Research workbench
2.7 ångström crystal structure of the nucleosome core particle assembled with a 146 bp alpha-satellite DNA (NCP146B) derivatized with TRIAMMINECHLOROPLATINUM(II) chloride
Analyse 2.7 ångström crystal structure of the nucleosome core particle assembled with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3REL
- Type
- protein + DNA
- Length
- 1,049 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.2; Histone H4; Histone H2A; Histone H2B 1.1; DNA (146-mer)
- UniProt
- P84233, P62799, P06897, P02281
- Ligands
- PT, MN, SO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 9 distinct chains · 63% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3.2 | protein | 98 | 64% helix, 4% strand | P84233 |
| B | Histone H4 | protein | 83 | 59% helix, 8% strand | P62799 |
| C | Histone H2A | protein | 103 | 58% helix, 6% strand | P06897 |
| D | Histone H2B 1.1 | protein | 99 | 71% helix, 4% strand | P02281 |
| E | Histone H3.2 | protein | 97 | 63% helix, 4% strand | P84233 |
| F | Histone H4 | protein | 78 | 59% helix, 8% strand | P62799 |
| G | Histone H2A | protein | 105 | 56% helix, 7% strand | P06897 |
| H | Histone H2B 1.1 | protein | 94 | 73% helix, 4% strand | P02281 |
| I, J | DNA (146-mer) | dna | 146 | — | — |
Ligands and binding sites
- PT · Platinum (II) ion · metal · 48 copies · chains J, I, F, B, H
- MN · Manganese (II) ion · metal · 2 copies · chains A, B, C, D
- 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1060 | 0.85 | 0.86 | 115 | empty |
| 2 | 737 | 0.79 | 0.83 | 78 | empty |
| 3 | 718 | 0.73 | 0.79 | 56 | PT |
| 4 | 709 | 0.67 | 0.76 | 54 | PT |
| 5 | 325 | 0.65 | 0.81 | 23 | empty |
Interfaces
36 interfaces between chains.
- I–J · 6474 Ų buried · 599 hydrogen bonds · nucleic-nucleic
- A–B · 2668 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 2652 Ų buried · 23 hydrogen bonds · protein-protein
- G–H · 2601 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 2576 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 3REL · 2.7 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 146 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 3REL · PDBe 3REL · UniProt P84233 · UniProt P62799 · UniProt P06897 · UniProt P02281
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