MolNFT v1 · #111317 · protein
Oxidized yfir
4YNA: “Oxidized yfir”. X-ray diffraction, 1 ligand (SO4), 9 pockets (best druggability 0.68). MolNFT v1 #111317 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4YNA
- Type
- protein
- Length
- 595 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yfir
- UniProt
- Q9I4L4
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Yfir | protein | 153 | 35% helix, 23% strand | Q9I4L4 |
| B | Yfir | protein | 148 | 32% helix, 24% strand | Q9I4L4 |
| C | Yfir | protein | 149 | 36% helix, 24% strand | Q9I4L4 |
| D | Yfir | protein | 145 | 28% 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
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 442 | 0.68 | 0.80 | 58 | empty |
| 2 | 67 | 0.47 | 0.83 | 14 | empty |
| 3 | 77 | 0.45 | 0.82 | 19 | empty |
| 4 | 78 | 0.41 | 0.79 | 19 | empty |
| 5 | 110 | 0.41 | 0.77 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–B · 747 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 701 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 451 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 136 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4YNA · Oxidized YfiR · 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 4YNA · PDBe 4YNA · UniProt Q9I4L4
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