Research workbench
Crystal structure of protein of unknown function yhal from bacillus subtilis
Analyse Crystal structure of protein of unknown function yhal 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
- 1SED
- Type
- protein
- Length
- 334 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein yhai
- UniProt
- O07517
- Ligands
- ZN, NA
- Pockets
- 2 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hypothetical protein yhai | protein | 112 | 72% helix, 0% strand | O07517 |
| B | Hypothetical protein yhai | protein | 110 | 73% helix, 0% strand | O07517 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- NA · Sodium ion · metal · 3 copies · chains A, B, C
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 17 copies · chains A, B, C
- GOL · Glycerol · additive · 6 copies · chains A, B, C
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 | 83 | 0.60 | 0.88 | 19 | empty |
| 2 | 118 | 0.40 | 0.75 | 21 | MPD |
Interfaces
3 interfaces between chains.
- A–C · 867 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 862 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 855 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1SED · Crystal Structure of Protein of Unknown Function YhaL from Bacillus subtilis · the same entry in another collection · chain A against A, TM-score 1.00
- O07517 · AlphaFold monomer V2.0 prediction for uncharacterized protein yhai (O07517) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 O07517
- Elsewhere: RCSB PDB 1SED · PDBe 1SED · UniProt O07517
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