MolNFT v1 · #111316 · protein
Yfir mutant-C110S
4YN9: “Yfir mutant-C110S”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.46). MolNFT v1 #111316 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4YN9
- Type
- protein
- Length
- 301 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yfir
- UniProt
- Q9I4L4
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Yfir | protein | 153 | 33% helix, 24% strand | Q9I4L4 |
| B | Yfir | protein | 148 | 33% helix, 25% strand | Q9I4L4 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
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 | 171 | 0.46 | 0.76 | 23 | empty |
| 2 | 77 | 0.42 | 0.80 | 16 | empty |
| 3 | 99 | 0.41 | 0.77 | 20 | empty |
| 4 | 59 | 0.38 | 0.80 | 14 | empty |
| 5 | 91 | 0.37 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 745 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4YN9 · YfiR mutant-C110S · 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 Q9I4L4
- Elsewhere: RCSB PDB 4YN9 · PDBe 4YN9 · UniProt Q9I4L4
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