MolNFT v1 · #66644 · protein
Crystal structure of siderocalin (ngal, lipocalin 2) complexed with fe-TRENCAM2-hopo
3HWF · Neutrophil gelatinase-associated lipocalin: “Crystal structure of siderocalin (ngal, lipocalin 2) complexed with fe-TRENCAM2-hopo”. X-ray diffraction, 5 ligands (TC2, NA, FE), 6 pockets (best druggability 0.52). MolNFT v1 #66644 on…
- PDB
- 3HWF
- 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
- TC2, NA, FE, SO4, CL
- Pockets
- 6 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Neutrophil gelatinase-associated lipocalin | protein | 173 | 13% helix, 43% strand | P80188 |
| B | Neutrophil gelatinase-associated lipocalin | protein | 169 | 12% helix, 43% strand | P80188 |
Ligands and binding sites
- TC2 · N-{2-[bis(2-{[(2,3-dihydroxyphenyl)carbonyl]amino}ethyl)amino]ethyl}-1-hydroxy-6-oxo-1,6-dihydropyridine-2-carboxamide · ligand · 3 copies · chains A, B, C
- NA · Sodium ion · metal · 4 copies · chains A, B, C
- FE · Fe (III) ion · metal · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 4 copies · chains A, C
- CL · Chloride ion · ion · 2 copies · chains A, C
- GOL · Glycerol · additive · 3 copies · chains 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 193 | 0.52 | 0.77 | 28 | FE, SO4, TC2, CL |
| 2 | 184 | 0.52 | 0.77 | 28 | FE, SO4, TC2, CL |
| 3 | 135 | 0.45 | 0.76 | 24 | FE, TC2 |
| 4 | 94 | 0.36 | 0.75 | 26 | empty |
| 5 | 104 | 0.36 | 0.74 | 23 | empty |
Interfaces
2 interfaces between chains.
- A–C · 383 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 66 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3HWF · Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with Fe-TrenCam2-hopo · 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 3HWF · PDBe 3HWF · UniProt P80188
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