MolNFT v1 · #75038 · protein
Siderocalin recognitin of carboxymycobactins: interference by the immune system in intracellular iron acquisition by mycobacteria tuberculosis
3PED · Neutrophil gelatinase-associated lipocalin: “Siderocalin recognitin of carboxymycobactins: interference by the immune system in intracellular iron…”. X-ray diffraction, 3 ligands (ZYF, FE, SO4), 6 pockets (best druggability 0.64).…
- PDB
- 3PED
- Type
- protein
- Length
- 521 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neutrophil gelatinase-associated lipocalin
- UniProt
- P80188
- Ligands
- ZYF, FE, SO4
- Pockets
- 6 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neutrophil gelatinase-associated lipocalin | protein | 177 | 15% helix, 42% strand | P80188 |
| B | Neutrophil gelatinase-associated lipocalin | protein | 172 | 15% helix, 44% strand | P80188 |
| C | Neutrophil gelatinase-associated lipocalin | protein | 172 | 15% helix, 44% strand | P80188 |
Ligands and binding sites
- ZYF · (9Z)-11-{hydroxy[(5S)-6-{[(1S)-3-{[(3S)-1-hydroxy-2-oxoazepan-3-yl]amino}-1-methyl-3-oxopropyl]oxy}-5-({[(4S)-2-(2-hydroxyphenyl)-4,5-dihydro-1,3-oxazol-4-yl]carbonyl}amino)-6-oxohexyl]amino}-11-oxoundec-9-enoic acid · ligand · 3 copies · chains A, B, C
- FE · Fe (III) ion · metal · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 357 | 0.64 | 0.79 | 33 | FE, ZYF |
| 2 | 358 | 0.64 | 0.79 | 35 | FE, ZYF |
| 3 | 342 | 0.62 | 0.78 | 31 | FE, ZYF |
| 4 | 171 | 0.43 | 0.73 | 20 | empty |
| 5 | 145 | 0.42 | 0.75 | 28 | empty |
Interfaces
2 interfaces between chains.
- A–C · 399 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 125 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3PED · Siderocalin Recognitin of Carboxymycobactins: Interference by the immune system in… · 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 3PED · PDBe 3PED · UniProt P80188
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.