MolNFT v1 · #117538 · protein
The yfib-yfir complex
5EB1: “The yfib-yfir complex”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.60). MolNFT v1 #117538 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5EB1
- Type
- protein
- Length
- 543 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yfir; Yfib
- UniProt
- Q9I4L4, Q9I4L6
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Yfir | protein | 147 | 33% helix, 25% strand | Q9I4L4 |
| B, D | Yfib | protein | 124 | 44% helix, 15% strand | Q9I4L6 |
| C | Yfir | protein | 148 | 32% helix, 25% strand | Q9I4L4 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 205 | 0.60 | 0.81 | 29 | empty |
| 2 | 211 | 0.59 | 0.81 | 24 | empty |
| 3 | 89 | 0.35 | 0.75 | 18 | empty |
| 4 | 83 | 0.35 | 0.75 | 18 | empty |
| 5 | 54 | 0.27 | 0.74 | 14 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1645 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1641 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 633 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5EB1 · the YfiB-YfiR complex · 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
- Every structure of UniProt Q9I4L6
- Elsewhere: RCSB PDB 5EB1 · PDBe 5EB1 · UniProt Q9I4L4 · UniProt Q9I4L6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.