Research workbench
Periplasmic repressor protein yfir
Analyse Periplasmic repressor protein yfir in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XJY
- Type
- protein
- Length
- 595 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yfir
- UniProt
- Q9I4L4
- Pockets
- 16 · best druggability 0.51
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Yfir | protein | 146 | 28% helix, 25% strand | Q9I4L4 |
| B | Yfir | protein | 148 | 31% helix, 24% strand | Q9I4L4 |
| C | Yfir | protein | 154 | 32% helix, 23% strand | Q9I4L4 |
| D | Yfir | protein | 147 | 31% helix, 24% strand | Q9I4L4 |
Ligands and binding sites
- TLA · L(+)-tartaric acid · additive · 3 copies · chains A, B, C, D
- P33 · 3,6,9,12,15,18-hexaoxaicosane-1,20-diol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 228 | 0.51 | 0.76 | 43 | empty |
| 2 | 108 | 0.47 | 0.80 | 19 | empty |
| 3 | 102 | 0.45 | 0.79 | 15 | empty |
| 4 | 95 | 0.44 | 0.79 | 16 | empty |
| 5 | 99 | 0.41 | 0.77 | 18 | empty |
Interfaces
3 interfaces between chains.
- C–D · 748 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 735 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 174 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 8 modified (disulfide, engineered).
Compared structures
- 4XJY · Periplasmic repressor protein 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 4XJY · PDBe 4XJY · UniProt Q9I4L4
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