Research workbench
Neutrophil gelatinase-associated lipocalin is a novel bacteriostatic agent that interferes with siderophore-mediated iron acquisition
Analyse Neutrophil gelatinase-associated lipocalin is a novel bacteriostatic agent that… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1L6M
- Type
- protein
- Length
- 515 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neutrophil gelatinase-associated lipocalin
- UniProt
- P80188
- Ligands
- DBH, DBS, FE, SO4
- Pockets
- 8 · best druggability 0.56
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 | 12% helix, 43% strand | P80188 |
| B | Neutrophil gelatinase-associated lipocalin | protein | 169 | 14% helix, 44% strand | P80188 |
| C | Neutrophil gelatinase-associated lipocalin | protein | 172 | 15% helix, 42% strand | P80188 |
Ligands and binding sites
- DBH · 2,3-dihydroxy-benzoic acid · ligand · 5 copies · chains A, B, C
- DBS · 2-(2,3-dihydroxy-benzoylamino)-3-hydroxy-propionic acid · ligand · 3 copies · chains A, B, C
- FE · Fe (III) ion · metal · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 208 | 0.56 | 0.79 | 34 | FE, DBH, DBS |
| 2 | 193 | 0.52 | 0.77 | 27 | FE, DBH, DBS |
| 3 | 188 | 0.49 | 0.76 | 23 | empty |
| 4 | 161 | 0.48 | 0.77 | 27 | FE, DBH, DBS |
| 5 | 75 | 0.41 | 0.79 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–C · 403 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 265 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1L6M · Neutrophil Gelatinase-associated Lipocalin is a Novel Bacteriostatic Agent that… · 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 1L6M · PDBe 1L6M · UniProt P80188
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