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Structure of the periplasmic binding protein afua from actinobacillus pleuropneumoniae (exogenous fructose-6-phosphate bound)
Analyse Structure of the periplasmic binding protein afua from actinobacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R74
- Type
- protein
- Length
- 1,277 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ABC-type FE3+ transport system, periplasmic component
- UniProt
- A3N294
- Ligands
- F6P, MG
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | ABC-type FE3+ transport system, periplasmic component | protein | 319 | 45% helix, 21% strand | A3N294 |
| B | ABC-type FE3+ transport system, periplasmic component | protein | 320 | 45% helix, 21% strand | A3N294 |
| C | ABC-type FE3+ transport system, periplasmic component | protein | 319 | 45% helix, 21% strand | A3N294 |
Ligands and binding sites
- F6P · 6-O-phosphono-beta-D-fructofuranose · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 3 copies · chains B, D
- GOL · Glycerol · additive · 18 copies · chains A, B, D, C
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 3 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 168 | 0.76 | 0.93 | 38 | F6P, GOL, MG |
| 2 | 531 | 0.75 | 0.83 | 75 | F6P, GOL |
| 3 | 326 | 0.75 | 0.87 | 57 | F6P, GOL, MG |
| 4 | 137 | 0.69 | 0.90 | 32 | F6P, GOL |
| 5 | 256 | 0.48 | 0.73 | 32 | empty |
Interfaces
4 interfaces between chains.
- A–B · 670 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 628 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 576 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 113 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4R74 · 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 4R74 · PDBe 4R74 · UniProt A3N294
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