MolNFT v1 · #113387 · protein
The periplasmic binding protein ceue of campylobacter jejuni preferentially binds the IRON(III) complex of the linear dimer component of enterobactin
5ADW · Enterochelin uptake periplasmic binding protein: “The periplasmic binding protein ceue of campylobacter jejuni preferentially binds the IRON(III) complex of…”. X-ray diffraction, 2 ligands (EHS, FE), 6 pockets (best druggability…
- PDB
- 5ADW
- 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
- EHS, FE
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Enterochelin uptake periplasmic binding protein | protein | 287 | 41% helix, 21% strand | Q0P8Q4 |
Ligands and binding sites
- EHS · 2S-2-[(2,3-dihydroxyphenyl)carbonylamino]-3-[(2S)-2-[(2,3-dihydroxyphenyl)carbonylamino]-3-hydroxy-propanoyl]oxy-propanoic acid · ligand · 2 copies · chains A, B
- FE · Fe (III) ion · metal · 3 copies · chains A, B, C
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 588 | 0.74 | 0.82 | 79 | FE |
| 2 | 722 | 0.67 | 0.75 | 73 | empty |
| 3 | 348 | 0.67 | 0.81 | 54 | FE, EHS, DMS |
| 4 | 268 | 0.66 | 0.83 | 42 | empty |
| 5 | 300 | 0.62 | 0.80 | 36 | empty |
Interfaces
3 interfaces between chains.
- A–C · 536 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 306 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 294 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5ADW · The Periplasmic Binding Protein CeuE of Campylobacter jejuni preferentially binds the… · 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 Q0P8Q4
- Elsewhere: RCSB PDB 5ADW · PDBe 5ADW · UniProt Q0P8Q4
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