MolNFT v1 · #105512 · protein
Structure of the periplasmic binding protein afua from actinobacillus pleuropneumoniae (endogenous glucose-6-phosphate and mannose-6- phosphate bound)
4R73 · ABC-type FE3+ transport system, periplasmic component: “Structure of the periplasmic binding protein afua from actinobacillus pleuropneumoniae (endogenous…”. X-ray diffraction, 3 ligands (M6P, G6P, CL), 5 pockets (best druggability…
- PDB
- 4R73
- Type
- protein
- Length
- 640 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ABC-type FE3+ transport system, periplasmic component
- UniProt
- A3N294
- Ligands
- M6P, G6P, CL
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ABC-type FE3+ transport system, periplasmic component | protein | 321 | 45% helix, 21% strand | A3N294 |
| B | ABC-type FE3+ transport system, periplasmic component | protein | 319 | 45% helix, 21% strand | A3N294 |
Ligands and binding sites
- M6P · 6-O-phosphono-alpha-D-mannopyranose · ligand · 2 copies · chains A, B
- G6P · 6-O-phosphono-alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 283 | 0.74 | 0.87 | 55 | G6P, M6P, CL |
| 2 | 113 | 0.66 | 0.90 | 32 | G6P, M6P, CL |
| 3 | 120 | 0.52 | 0.82 | 25 | GOL |
| 4 | 70 | 0.29 | 0.73 | 14 | empty |
| 5 | 56 | 0.24 | 0.72 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 694 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4R73 · Structure of the periplasmic binding protein AfuA from Actinobacillus pleuropneumoniae… · 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 A3N294
- Elsewhere: RCSB PDB 4R73 · PDBe 4R73 · UniProt A3N294
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