Research workbench
The periplasmic binding protein ceue of campylobacter jejuni preferentially binds the IRON(III) complex of the linear dimer component of enterobactin
Analyse The periplasmic binding protein ceue of campylobacter jejuni preferentially… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ADV
- Type
- protein
- Length
- 861 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Enterochelin uptake periplasmic binding protein
- UniProt
- Q0P8Q4
- Ligands
- DBS, EHS, FE
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Enterochelin uptake periplasmic binding protein | protein | 287 | 42% helix, 21% strand | Q0P8Q4 |
Ligands and binding sites
- DBS · 2-(2,3-dihydroxy-benzoylamino)-3-hydroxy-propionic acid · ligand · 4 copies · chains A, B, C
- EHS · 2S-2-[(2,3-dihydroxyphenyl)carbonylamino]-3-[(2S)-2-[(2,3-dihydroxyphenyl)carbonylamino]-3-hydroxy-propanoyl]oxy-propanoic acid · ligand · chains B
- FE · Fe (III) ion · metal · 3 copies · chains A, B, C
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A, B
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 | 924 | 0.74 | 0.78 | 95 | DMS, FE, DBS |
| 2 | 337 | 0.66 | 0.81 | 50 | FE, DBS |
| 3 | 230 | 0.63 | 0.82 | 36 | FE, DBS, DMS |
| 4 | 351 | 0.59 | 0.76 | 30 | empty |
| 5 | 197 | 0.46 | 0.74 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–C · 518 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 295 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 284 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5ADV · The Periplasmic Binding Protein CeuE of Campylobacter jejuni preferentially binds the… · the same entry in another collection · chain C against C, 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 Q0P8Q4
- Elsewhere: RCSB PDB 5ADV · PDBe 5ADV · UniProt Q0P8Q4
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