Research workbench
The structure of human siderocalin bound to the bacterial siderophore fluvibactin
Analyse The structure of human siderocalin bound to the bacterial siderophore… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K19
- Type
- protein
- Length
- 513 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neutrophil gelatinase-associated lipocalin
- UniProt
- P80188
- Ligands
- 1OD, FE, NA, SO4, CL
- Pockets
- 9 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neutrophil gelatinase-associated lipocalin | protein | 174 | 13% helix, 44% strand | P80188 |
| B | Neutrophil gelatinase-associated lipocalin | protein | 163 | 12% helix, 43% strand | P80188 |
| C | Neutrophil gelatinase-associated lipocalin | protein | 176 | 15% helix, 43% strand | P80188 |
Ligands and binding sites
- 1OD · (4S,5R)-N,N-bis{3-[(2,3-dihydroxybenzoyl)amino]propyl}-2-(2,3-dihydroxyphenyl)-5-methyl-4,5-dihydro-1,3-oxazole-4-carboxamide · ligand · 3 copies · chains A, B, C
- FE · Fe (III) ion · metal · 3 copies · chains A, B, C
- NA · Sodium ion · metal · 2 copies · chains C
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
- CL · Chloride ion · ion · 2 copies · chains A, C
- GOL · Glycerol · additive · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 248 | 0.58 | 0.78 | 39 | FE, 1OD |
| 2 | 237 | 0.53 | 0.76 | 30 | FE, SO4, 1OD |
| 3 | 202 | 0.52 | 0.76 | 30 | FE, SO4, 1OD |
| 4 | 132 | 0.41 | 0.75 | 26 | empty |
| 5 | 75 | 0.39 | 0.77 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–C · 393 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 70 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4K19 · The structure of Human Siderocalin bound to the bacterial siderophore fluvibactin · 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 P80188
- Elsewhere: RCSB PDB 4K19 · PDBe 4K19 · UniProt P80188
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