MolNFT v1 · #114528 · protein
Structure of histone H3/H4 in complex with SPT2
5BS7 · Histone H3.2: “Structure of histone H3/H4 in complex with SPT2”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.45). MolNFT v1 #114528 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5BS7
- Type
- protein
- Length
- 380 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.2; Histone H4; Protein SPT2 homolog
- UniProt
- P84233, P62799, Q68D10
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.45
Structure
x-ray diffraction · 6 distinct chains · 65% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3.2 | protein | 75 | 69% helix, 3% strand | P84233 |
| B | Histone H3.2 | protein | 76 | 70% helix, 4% strand | P84233 |
| C | Histone H4 | protein | 69 | 62% helix, 3% strand | P62799 |
| D | Histone H4 | protein | 68 | 68% helix, 4% strand | P62799 |
| E | Protein SPT2 homolog | protein | 70 | 63% helix, 1% strand | Q68D10 |
| F | Protein SPT2 homolog | protein | 22 | 36% helix, 0% strand | Q68D10 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 96 | 0.45 | 0.80 | 19 | empty |
| 2 | 82 | 0.43 | 0.79 | 17 | empty |
| 3 | 76 | 0.41 | 0.79 | 15 | empty |
| 4 | 84 | 0.37 | 0.76 | 17 | empty |
| 5 | 103 | 0.34 | 0.73 | 17 | empty |
Interfaces
10 interfaces between chains.
- A–C · 1680 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 1636 Ų buried · 7 hydrogen bonds · protein-protein
- C–E · 817 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 641 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 581 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- Q68D10 · AlphaFold monomer V2.0 prediction for protein SPT2 homolog (Q68D10) · a predicted model of the same protein · chain E against A, TM-score 0.80
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 P84233
- Every structure of UniProt P62799
- Every structure of UniProt Q68D10
- Elsewhere: RCSB PDB 5BS7 · PDBe 5BS7 · UniProt P84233 · UniProt P62799 · UniProt Q68D10
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