MolNFT v1 · #174834 · protein
Structural insights into nucleosome reorganization by NAP1-related protein 1 (NRP1)
7C7X · Histone H2A.6: “Structural insights into nucleosome reorganization by NAP1-related protein 1 (NRP1)”. X-ray diffraction, 10 pockets (best druggability 0.58). MolNFT v1 #174834 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7C7X
- Type
- protein
- Length
- 683 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H2A.6; Histone H2B.1; NAP1-related protein 1
- UniProt
- Q9LD28, Q9LQQ4, Q9CA59
- Pockets
- 10 · best druggability 0.58
Structure
x-ray diffraction · 5 distinct chains · 60% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A | Histone H2A.6 | protein | 81 | 63% helix, 2% strand | Q9LD28 |
| D | Histone H2B.1 | protein | 90 | 73% helix, 2% strand | Q9LQQ4 |
| E | NAP1-related protein 1 | protein | 174 | 51% helix, 10% strand | Q9CA59 |
| F | NAP1-related protein 1 | protein | 166 | 51% helix, 12% strand | Q9CA59 |
| B | Histone H2B.1 | protein | 91 | 76% helix, 2% strand | Q9LQQ4 |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains D, F, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 324 | 0.58 | 0.77 | 40 | empty |
| 2 | 394 | 0.57 | 0.74 | 47 | empty |
| 3 | 119 | 0.56 | 0.83 | 16 | empty |
| 4 | 374 | 0.56 | 0.74 | 46 | empty |
| 5 | 196 | 0.53 | 0.78 | 27 | empty |
Interfaces
9 interfaces between chains.
- C–D · 1903 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1816 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1693 Ų buried · 15 hydrogen bonds · protein-protein
- D–F · 361 Ų buried · 6 hydrogen bonds · protein-protein
- E–B · 334 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7C7X · Structural insights into nucleosome reorganization by NAP1-RELATED PROTEIN 1 (NRP1) · the same entry in another collection · chain B against B, TM-score 1.00
- Q9CA59 · AlphaFold monomer V2.0 prediction for NAP1-related protein 1 (Q9CA59) · a predicted model of the same protein · chain F against A, TM-score 0.94
- Q9LD28 · AlphaFold monomer V2.0 prediction for histone H2A.6 (Q9LD28) · a predicted model of the same protein · chain C against A, TM-score 0.94
- Q9LQQ4 · AlphaFold monomer V2.0 prediction for histone H2B.1 (Q9LQQ4) · a predicted model of the same protein · chain D against A, TM-score 0.55
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
- Every structure of UniProt Q9CA59
- Elsewhere: RCSB PDB 7C7X · PDBe 7C7X · UniProt Q9LD28 · UniProt Q9LQQ4 · UniProt Q9CA59
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