MolNFT v1 · #75037 · protein
Siderocalin recognitin of carboxymycobactins: interference by the immune system in intracellular iron acquisition by mycobacteria tuberculosis
3PEC · Neutrophil gelatinase-associated lipocalin: “Siderocalin recognitin of carboxymycobactins: interference by the immune system in intracellular iron…”. X-ray diffraction, 4 ligands (ZYG, NA, FE), 7 pockets (best druggability 0.65).…
- PDB
- 3PEC
- Type
- protein
- Length
- 516 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neutrophil gelatinase-associated lipocalin
- UniProt
- P80188
- Ligands
- ZYG, NA, FE, SO4
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neutrophil gelatinase-associated lipocalin | protein | 176 | 13% helix, 43% strand | P80188 |
| B | Neutrophil gelatinase-associated lipocalin | protein | 165 | 13% helix, 45% strand | P80188 |
| C | Neutrophil gelatinase-associated lipocalin | protein | 175 | 15% helix, 43% strand | P80188 |
Ligands and binding sites
- ZYG · 9-{hydroxy[(5S,6R)-6-hydroxy-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)hexyl]amino}-9-oxononanoic acid · ligand · chains C
- NA · Sodium ion · metal · 4 copies · chains C
- FE · Fe (III) ion · metal · chains C
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 7 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 380 | 0.65 | 0.79 | 37 | FE, ZYG |
| 2 | 303 | 0.59 | 0.77 | 34 | empty |
| 3 | 200 | 0.55 | 0.78 | 30 | empty |
| 4 | 151 | 0.45 | 0.76 | 29 | NA |
| 5 | 125 | 0.42 | 0.76 | 24 | empty |
Interfaces
2 interfaces between chains.
- A–C · 400 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 88 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3PEC · 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 3PEC · PDBe 3PEC · UniProt P80188
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