MolNFT v1 · #58792 · protein
Crystal structure of fite (crystal form 2), a group III periplasmic siderophore binding protein
3BE6 · Putative iron compound-binding protein of ABC transporter…: “Crystal structure of fite (crystal form 2), a group III periplasmic siderophore binding protein”. X-ray diffraction, 2 ligands (MG, CL), 13 pockets (best druggability…
- PDB
- 3BE6
- Type
- protein
- Length
- 1,172 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative iron compound-binding protein of ABC transporter family
- UniProt
- Q8XBR1
- Ligands
- MG, CL
- Pockets
- 13 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Putative iron compound-binding protein of ABC transporter family | protein | 294 | 43% helix, 19% strand | Q8XBR1 |
| B, D | Putative iron compound-binding protein of ABC transporter family | protein | 292 | 42% helix, 18% strand | Q8XBR1 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · 7 copies · chains A, C, B, D
- GOL · Glycerol · additive · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 634 | 0.78 | 0.83 | 86 | CL |
| 2 | 510 | 0.75 | 0.83 | 49 | empty |
| 3 | 429 | 0.69 | 0.81 | 39 | empty |
| 4 | 225 | 0.64 | 0.83 | 33 | GOL |
| 5 | 176 | 0.58 | 0.82 | 33 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1906 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1862 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 1367 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified, 2 disulfide (engineered, disulfide).
Compared structures
- 3BE6 · Crystal structure of FitE (crystal form 2), a group III periplasmic siderophore binding… · 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 Q8XBR1
- Elsewhere: RCSB PDB 3BE6 · PDBe 3BE6 · UniProt Q8XBR1
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