MolNFT v1 · #174234 · protein
Structural mechanism directing nucleosome reorganization by NAP1- related protein 1 (NRP1)
7BP2 · Histone H2A.6: “Structural mechanism directing nucleosome reorganization by NAP1- related protein 1 (NRP1)”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.63). MolNFT v1 #174234 on GenesisL1: 3D structure…
- PDB
- 7BP2
- Type
- protein
- Length
- 352 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H2A.6; Histone H2B.1
- UniProt
- Q9LD28, Q9LQQ4
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 74% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Histone H2A.6 | protein | 87 | 67% helix, 5% strand | Q9LD28 |
| B | Histone H2B.1 | protein | 90 | 77% helix, 4% strand | Q9LQQ4 |
| D | Histone H2B.1 | protein | 88 | 78% helix, 5% strand | Q9LQQ4 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 10 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 348 | 0.63 | 0.79 | 40 | SO4 |
| 2 | 201 | 0.56 | 0.79 | 24 | GOL |
| 3 | 65 | 0.31 | 0.75 | 14 | empty |
| 4 | 62 | 0.30 | 0.74 | 14 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2428 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 2399 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 334 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 195 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 159 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7BP2 · Structural mechanism directing nucleosome reorganization by NAP1-RELATED PROTEIN 1 (NRP1) · the same entry in another collection · chain D against D, TM-score 1.00
- Q9LQQ4 · AlphaFold monomer V2.0 prediction for histone H2B.1 (Q9LQQ4) · a predicted model of the same protein · chain D against A, TM-score 0.97
- Q9LD28 · AlphaFold monomer V2.0 prediction for histone H2A.6 (Q9LD28) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 7BP2 · PDBe 7BP2 · UniProt Q9LD28 · UniProt Q9LQQ4
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