Research workbench
Crystal structure of a member of hit family of proteins from bacillus subtilis
Analyse Crystal structure of a member of hit family of proteins from bacillus subtilis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Y23
- Type
- protein
- Length
- 698 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histidine triad protein
- UniProt
- O07513
- Ligands
- ZN, MG
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Histidine triad protein | protein | 139 | 35% helix, 24% strand | O07513 |
| B, E | Histidine triad protein | protein | 141 | 35% helix, 23% strand | O07513 |
| C | Histidine triad protein | protein | 138 | 36% helix, 24% strand | O07513 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 347 | 0.61 | 0.78 | 55 | empty |
| 2 | 108 | 0.50 | 0.81 | 21 | empty |
| 3 | 142 | 0.42 | 0.74 | 31 | empty |
| 4 | 129 | 0.42 | 0.75 | 32 | empty |
| 5 | 128 | 0.40 | 0.74 | 30 | empty |
Interfaces
4 interfaces between chains.
- C–D · 3279 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 3277 Ų buried · 39 hydrogen bonds · protein-protein
- C–E · 673 Ų buried · 3 hydrogen bonds · protein-protein
- D–E · 41 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1Y23 · Crystal structure of a member of HIT family of proteins from bacillus subtilis · the same entry in another collection · chain E against E, TM-score 1.00
- O07513 · AlphaFold monomer V2.0 prediction for protein hit (O07513) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 O07513
- Elsewhere: RCSB PDB 1Y23 · PDBe 1Y23 · UniProt O07513
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