MolNFT v1 · #136806 · protein
Crystal structure of the protein of unknown function of the conserved rid protein family yyfb from yersinia pestis
5V4F · Putative translational inhibitor protein: “Crystal structure of the protein of unknown function of the conserved rid protein family yyfb from yersinia…”. X-ray diffraction, 4 pockets (best druggability 0.68). MolNFT v1 #136806 on…
- 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
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