Research workbench
Cryo-EM structure of the nucleosome containing Komagataella pastoris histones
Analyse Cryo-EM structure of the nucleosome containing Komagataella pastoris histones in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WLR
- Type
- protein + DNA
- Length
- 1,044 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.54
- Source
- Komagataella pastoris; SYNTHETIC CONSTRUCT
- Molecule
- Histone H3; Histone H4; Histone H2A; Histone H2B; DNA (145-mer)
- UniProt
- A0A1B2JB78, A0A1B2JA70, A0A1B2JD99, A0A1B2JBS1
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · resolution 3.54 · 9 distinct chains · 65% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Histone H3 | protein | 96 | 69% helix, 4% strand | A0A1B2JB78 |
| B | Histone H4 | protein | 83 | 61% helix, 8% strand | A0A1B2JA70 |
| C | Histone H2A | protein | 104 | 56% helix, 7% strand | A0A1B2JD99 |
| D | Histone H2B | protein | 95 | 75% helix, 4% strand | A0A1B2JBS1 |
| F | Histone H4 | protein | 82 | 62% helix, 9% strand | A0A1B2JA70 |
| G | Histone H2A | protein | 106 | 58% helix, 7% strand | A0A1B2JD99 |
| H | Histone H2B | protein | 92 | 77% helix, 4% strand | A0A1B2JBS1 |
| I | DNA (145-mer) | dna | 145 | — | — |
| J | DNA (145-mer) | dna | 145 | — | — |
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 | 690 | 0.78 | 0.83 | 69 | empty |
| 2 | 467 | 0.73 | 0.83 | 50 | empty |
| 3 | 412 | 0.72 | 0.83 | 38 | empty |
| 4 | 303 | 0.67 | 0.83 | 30 | empty |
| 5 | 418 | 0.67 | 0.80 | 38 | empty |
Interfaces
37 interfaces between chains.
- I–J · 6515 Ų buried · 507 hydrogen bonds · nucleic-nucleic
- E–F · 2625 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 2606 Ų buried · 22 hydrogen bonds · protein-protein
- G–H · 2594 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 2587 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 7WLR · Cryo-EM structure of the nucleosome containing komagataella pastoris histones · the same entry in another collection · chain A against A, 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 A0A1B2JB78
- Every structure of UniProt A0A1B2JA70
- Every structure of UniProt A0A1B2JD99
- Every structure of UniProt A0A1B2JBS1
- Elsewhere: RCSB PDB 7WLR · PDBe 7WLR · UniProt A0A1B2JB78 · UniProt A0A1B2JA70 · UniProt A0A1B2JD99 · UniProt A0A1B2JBS1
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