Research workbench
Using soft X-rays for a detailed picture of divalent metal binding in the nucleosome
Analyse Using soft X-rays for a detailed picture of divalent metal binding in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LJA
- Type
- protein + DNA
- Length
- 1,066 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; 147MER DNA
- UniProt
- P84233, P62799, Q6AZJ8, P02281
- Ligands
- MN, SO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 8 distinct chains · 61% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Histone H3.2 | protein | 99 | 62% helix, 4% strand | P84233 |
| B | Histone H4 | protein | 79 | 62% helix, 9% strand | P62799 |
| C | Histone H2A | protein | 104 | 58% helix, 7% strand | Q6AZJ8 |
| D, H | Histone H2B 1.1 | protein | 99 | 71% helix, 4% strand | P02281 |
| F | Histone H4 | protein | 87 | 57% helix, 8% strand | P62799 |
| G | Histone H2A | protein | 106 | 55% helix, 7% strand | Q6AZJ8 |
| I | 147MER DNA | dna | 147 | — | — |
| J | 147MER DNA | dna | 147 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 45 copies · chains E, F, J, I, G, H
- SO4 · Sulfate ion · ion · 3 copies · chains G, H, I, C, D, J
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 | 983 | 0.84 | 0.85 | 89 | empty |
| 2 | 417 | 0.78 | 0.87 | 46 | empty |
| 3 | 429 | 0.76 | 0.85 | 44 | empty |
| 4 | 730 | 0.74 | 0.80 | 59 | MN, SO4 |
| 5 | 631 | 0.67 | 0.77 | 60 | MN |
Interfaces
37 interfaces between chains.
- I–J · 6522 Ų buried · 642 hydrogen bonds · nucleic-nucleic
- C–D · 2657 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 2655 Ų buried · 28 hydrogen bonds · protein-protein
- G–H · 2655 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 2502 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 3LJA · Using Soft X-Rays for a Detailed Picture of Divalent Metal Binding in the Nucleosome · the same entry in another collection · chain J against J, 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 0.98
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 Q6AZJ8
- Every structure of UniProt P02281
- Elsewhere: RCSB PDB 3LJA · PDBe 3LJA · UniProt P84233 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281
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