MolNFT v1 · #64193 · protein
Crystal structure of siderocalin (ngal, lipocalin 2) complexed with ferric 4-methyl-catechol
3FW5 · Neutrophil gelatinase-associated lipocalin: “Crystal structure of siderocalin (ngal, lipocalin 2) complexed with ferric 4-methyl-catechol”. X-ray diffraction, 4 ligands (MCT, NA, FE), 6 pockets (best druggability 0.52). MolNFT v1…
- PDB
- 3FW5
- Type
- protein
- Length
- 510 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neutrophil gelatinase-associated lipocalin
- UniProt
- P80188
- Ligands
- MCT, NA, FE, CL
- Pockets
- 6 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neutrophil gelatinase-associated lipocalin | protein | 175 | 13% helix, 43% strand | P80188 |
| B | Neutrophil gelatinase-associated lipocalin | protein | 161 | 11% helix, 46% strand | P80188 |
| C | Neutrophil gelatinase-associated lipocalin | protein | 174 | 15% helix, 43% strand | P80188 |
Ligands and binding sites
- MCT · 4-methylcatechol · ligand · 3 copies · chains A, B, C
- NA · Sodium ion · metal · 7 copies · chains A, C
- FE · Fe (III) ion · metal · 3 copies · chains A, B, C
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 9 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 202 | 0.52 | 0.77 | 31 | FE, MCT |
| 2 | 173 | 0.51 | 0.77 | 28 | FE, MCT |
| 3 | 191 | 0.49 | 0.75 | 38 | FE, MCT, CL |
| 4 | 118 | 0.38 | 0.74 | 24 | NA, GOL |
| 5 | 78 | 0.35 | 0.76 | 24 | NA |
Interfaces
2 interfaces between chains.
- A–C · 404 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 55 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3FW5 · Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with Ferric… · 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 3FW5 · PDBe 3FW5 · UniProt P80188
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.