MolNFT v1 · #119842 · protein
Crystal structure of FE3+ - desferal bound siderophore binding protein fhud from vibrio cholerae
5GGX · IRON(III) ABC transporter, periplasmic iron-compound…: “Crystal structure of FE3+ - desferal bound siderophore binding protein fhud from vibrio cholerae”. X-ray diffraction, 1 ligand (DEF), 8 pockets (best druggability 0.78). MolNFT…
- PDB
- 5GGX
- Type
- protein
- Length
- 1,064 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IRON(III) ABC transporter, periplasmic iron-compound- binding protein
- UniProt
- A0A0H3AJ03
- Ligands
- DEF
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | IRON(III) ABC transporter, periplasmic iron-compound- binding protein | protein | 265 | 41% helix, 17% strand | A0A0H3AJ03 |
| B, C | IRON(III) ABC transporter, periplasmic iron-compound- binding protein | protein | 266 | 44% helix, 17% strand | A0A0H3AJ03 |
| D | IRON(III) ABC transporter, periplasmic iron-compound- binding protein | protein | 267 | 43% helix, 18% strand | A0A0H3AJ03 |
Ligands and binding sites
- DEF · Deferoxamine mesylate fe(iii) complex · ligand · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 932 | 0.78 | 0.80 | 85 | DEF |
| 2 | 824 | 0.76 | 0.80 | 69 | empty |
| 3 | 124 | 0.52 | 0.81 | 17 | empty |
| 4 | 264 | 0.51 | 0.74 | 32 | DEF |
| 5 | 113 | 0.39 | 0.75 | 18 | DEF |
Interfaces
5 interfaces between chains.
- B–D · 962 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 583 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 538 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 484 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 214 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5GGX · Crystal Structure of Fe3+ - Desferal bound siderophore binding protein FhuD from Vibrio… · 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 A0A0H3AJ03
- Elsewhere: RCSB PDB 5GGX · PDBe 5GGX · UniProt A0A0H3AJ03
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