MolNFT v1 · #66645 · protein
Crystal structure of siderocalin (ngal, lipocalin 2) complexed with fe-trencam-HOPO2
3HWG · Neutrophil gelatinase-associated lipocalin: “Crystal structure of siderocalin (ngal, lipocalin 2) complexed with fe-trencam-HOPO2”. X-ray diffraction, 5 ligands (QED, NA, FE), 5 pockets (best druggability 0.58). MolNFT v1 #66645 on…
- PDB
- 3HWG
- 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
- QED, NA, FE, SO4, CL
- Pockets
- 5 · best druggability 0.58
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 | 175 | 13% helix, 43% strand | P80188 |
| B | Neutrophil gelatinase-associated lipocalin | protein | 167 | 14% helix, 46% strand | P80188 |
| C | Neutrophil gelatinase-associated lipocalin | protein | 174 | 15% helix, 43% strand | P80188 |
Ligands and binding sites
- QED · N,N'-{[(2-{[(2,3-dihydroxyphenyl)carbonyl]amino}ethyl)imino]diethane-2,1-diyl}bis(1-hydroxy-6-oxo-1,6-dihydropyridine-2 -carboxamide) · ligand · 3 copies · chains A, B, C
- NA · Sodium ion · metal · 8 copies · chains A, C
- FE · Fe (III) ion · metal · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C
- CL · Chloride ion · ion · chains C
- GOL · Glycerol · additive · 12 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 405 | 0.58 | 0.74 | 50 | FE, QED, SO4 |
| 2 | 248 | 0.56 | 0.77 | 29 | FE, QED, SO4 |
| 3 | 214 | 0.53 | 0.77 | 34 | FE, QED, GOL, SO4 |
| 4 | 133 | 0.40 | 0.75 | 25 | GOL |
| 5 | 60 | 0.28 | 0.74 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–C · 402 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 117 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3HWG · Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with Fe-TrenCam-hopo2 · 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 3HWG · PDBe 3HWG · UniProt P80188
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