Research workbench
Structural insights into nucleosome reorganization by NAP1-related protein 1 (NRP1)
Analyse Structural insights into nucleosome reorganization by NAP1-related protein 1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BP4
- Type
- protein
- Length
- 352 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H2A.6; Histone H2B.1; Asp-asp-asp-asp-tyr
- UniProt
- Q9LD28, Q9LQQ4
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · 5 distinct chains · 69% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Histone H2A.6 | protein | 82 | 63% helix, 5% strand | Q9LD28 |
| H | Histone H2B.1 | protein | 88 | 77% helix, 6% strand | Q9LQQ4 |
| L, C | Asp-asp-asp-asp-tyr | protein | 5 | 0% helix, 20% strand | — |
| A | Histone H2A.6 | protein | 83 | 64% helix, 5% strand | Q9LD28 |
| B | Histone H2B.1 | protein | 89 | 75% helix, 6% strand | Q9LQQ4 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 441 | 0.63 | 0.77 | 48 | empty |
| 2 | 57 | 0.28 | 0.74 | 12 | empty |
Interfaces
10 interfaces between chains.
- A–B · 2498 Ų buried · 25 hydrogen bonds · protein-protein
- G–H · 2452 Ų buried · 19 hydrogen bonds · protein-protein
- H–L · 298 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 292 Ų buried · 7 hydrogen bonds · protein-protein
- G–A · 221 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7BP4 · Structural insights into nucleosome reorganization by NAP1-RELATED PROTEIN 1 (NRP1) · the same entry in another collection · chain C against C, TM-score 1.00
- Q9LQQ4 · AlphaFold monomer V2.0 prediction for histone H2B.1 (Q9LQQ4) · a predicted model of the same protein · chain H against A, TM-score 0.95
- Q9LD28 · AlphaFold monomer V2.0 prediction for histone H2A.6 (Q9LD28) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 Q9LD28
- Every structure of UniProt Q9LQQ4
- Elsewhere: RCSB PDB 7BP4 · PDBe 7BP4 · UniProt Q9LD28 · UniProt Q9LQQ4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.