Research workbench
Crystal structure of the protein of unknown function of the conserved rid protein family yyfb from yersinia pestis
Analyse Crystal structure of the protein of unknown function of the conserved rid… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V4F
- Type
- protein
- Length
- 266 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative translational inhibitor protein
- UniProt
- Q7CGF8
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative translational inhibitor protein | protein | 133 | 29% helix, 30% strand | Q7CGF8 |
Ligands and binding sites
- GOL · Glycerol · additive · 12 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 200 | 0.68 | 0.86 | 35 | empty |
| 2 | 81 | 0.33 | 0.74 | 20 | empty |
| 3 | 77 | 0.29 | 0.73 | 21 | empty |
| 4 | 61 | 0.27 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 823 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 5V4F · Crystal Structure of the Protein of Unknown Function of the Conserved Rid Protein Family… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q7CGF8
- Elsewhere: RCSB PDB 5V4F · PDBe 5V4F · UniProt Q7CGF8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.