Research workbench
A complex of the synthetic siderophore analogue FE(III)-5-licam with ceue (H227L variant), a periplasmic protein from campylobacter jejuni.
Analyse A complex of the synthetic siderophore analogue FE(III)-5-licam with ceue… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TCY
- Type
- protein
- Length
- 866 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Enterochelin uptake periplasmic binding protein
- UniProt
- A0A0W8LI20
- Ligands
- 5LC, FE
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Enterochelin uptake periplasmic binding protein | protein | 289 | 41% helix, 21% strand | A0A0W8LI20 |
| B | Enterochelin uptake periplasmic binding protein | protein | 289 | 40% helix, 21% strand | A0A0W8LI20 |
| C | Enterochelin uptake periplasmic binding protein | protein | 288 | 42% helix, 20% strand | A0A0W8LI20 |
Ligands and binding sites
- 5LC · N,N'-pentane-1,5-diylbis(2,3-dihydroxybenzamide) · ligand · 3 copies · chains A, B, C
- FE · Fe (III) ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1031 | 0.77 | 0.79 | 108 | FE, 5LC |
| 2 | 198 | 0.63 | 0.83 | 29 | empty |
| 3 | 367 | 0.59 | 0.76 | 34 | empty |
| 4 | 291 | 0.57 | 0.77 | 38 | empty |
| 5 | 122 | 0.47 | 0.79 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–C · 478 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 345 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 165 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5TCY · A complex of the synthetic siderophore analogue Fe(III)-5-LICAM with CeuE (H227L… · 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 A0A0W8LI20
- Elsewhere: RCSB PDB 5TCY · PDBe 5TCY · UniProt A0A0W8LI20
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.