Research workbench
Fitting of the H2A-H2B histones in the electron microscopy MAP of the complex NUCLEOPLASMIN:H2A-H2B histones (1:5).
Analyse Fitting of the H2A-H2B histones in the electron microscopy MAP of the complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XQL
- Type
- protein
- Length
- 905 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H2A-IV; Histone H2B 5
- UniProt
- P02263, P0C1H4
- Pockets
- 10 · best druggability 0.52
Structure
electron microscopy · 2 distinct chains · 70% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I | Histone H2A-IV | protein | 91 | 64% helix, 4% strand | P02263 |
| B, D, F, H, J | Histone H2B 5 | protein | 90 | 76% helix, 4% strand | P0C1H4 |
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 177 | 0.52 | 0.78 | 36 | empty |
| 2 | 198 | 0.52 | 0.77 | 40 | empty |
| 3 | 196 | 0.51 | 0.77 | 38 | empty |
| 4 | 176 | 0.51 | 0.77 | 38 | empty |
| 5 | 180 | 0.50 | 0.77 | 38 | empty |
Interfaces
25 interfaces between chains.
- G–H · 2601 Ų buried · 31 hydrogen bonds · protein-protein
- I–J · 2600 Ų buried · 31 hydrogen bonds · protein-protein
- E–F · 2598 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 2597 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 2588 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 2XQL · Fitting of the H2A-H2B histones in the electron microscopy map of the complex… · the same entry in another collection · chain J against J, TM-score 1.00
- P02263 · AlphaFold monomer V2.0 prediction for histone H2A-IV (P02263) · a predicted model of the same protein · chain A against A, TM-score 0.97
- P0C1H4 · AlphaFold monomer V2.0 prediction for histone H2B 5 (P0C1H4) · a predicted model of the same protein · chain B against A, TM-score 0.90
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 P02263
- Every structure of UniProt P0C1H4
- Elsewhere: RCSB PDB 2XQL · PDBe 2XQL · UniProt P02263 · UniProt P0C1H4
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