Research workbench
Yfib-yfir complexed with gmp
Analyse Yfib-yfir complexed with gmp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y61
- Type
- protein
- Length
- 552 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yfir; Yfib
- UniProt
- Q9I4L4, Q9I4L6
- Ligands
- 5GP
- Pockets
- 8 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Yfir | protein | 153 | 35% helix, 24% strand | Q9I4L4 |
| B, D | Yfib | protein | 123 | 43% helix, 17% strand | Q9I4L6 |
Ligands and binding sites
- 5GP · Guanosine-5'-monophosphate · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 217 | 0.60 | 0.81 | 27 | empty |
| 2 | 186 | 0.57 | 0.81 | 25 | empty |
| 3 | 50 | 0.45 | 0.85 | 16 | empty |
| 4 | 86 | 0.36 | 0.76 | 18 | empty |
| 5 | 77 | 0.32 | 0.74 | 17 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1681 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1676 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 752 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 modified (disulfide, engineered).
Compared structures
- 5Y61 · YfiB-YfiR complexed with GMP · 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 5Y61 · PDBe 5Y61 · UniProt Q9I4L4 · UniProt Q9I4L6
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