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The crystal structure of a flagella protein from yersinia enterocolitica subsp. enterocolitica 8081
Analyse The crystal structure of a flagella protein from yersinia enterocolitica subsp.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NKZ
- Type
- protein
- Length
- 385 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Flagellar protein flit
- UniProt
- A1JSR8
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 88% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Flagellar protein flit | protein | 97 | 87% helix, 0% strand | A1JSR8 |
| C | Flagellar protein flit | protein | 95 | 89% helix, 0% strand | A1JSR8 |
| D | Flagellar protein flit | protein | 96 | 89% helix, 0% strand | A1JSR8 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B, C, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 211 | 0.83 | 0.96 | 26 | PG4 |
| 2 | 204 | 0.83 | 0.96 | 26 | PG4 |
| 3 | 656 | 0.79 | 0.84 | 60 | SO4 |
| 4 | 168 | 0.75 | 0.91 | 30 | empty |
| 5 | 250 | 0.72 | 0.86 | 35 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2082 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 2044 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 401 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 157 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 154 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 3NKZ · The crystal structure of a flagella protein from Yersinia enterocolitica subsp.… · the same entry in another collection · chain D against D, TM-score 1.00
- A1JSR8 · AlphaFold monomer V2.0 prediction for flagellar protein flit (A1JSR8) · a predicted model of the same protein · chain B against A, TM-score 0.57
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 A1JSR8
- Elsewhere: RCSB PDB 3NKZ · PDBe 3NKZ · UniProt A1JSR8
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