MolNFT v1 · #112305 · protein
Siderocalin-mediated recognition and cellular uptake of actinides
4ZHC · Neutrophil gelatinase-associated lipocalin: “Siderocalin-mediated recognition and cellular uptake of actinides”. X-ray diffraction, 3 ligands (TC2, TH, SO4), 6 pockets (best druggability 0.56). MolNFT v1 #112305 on GenesisL1: 3D…
- PDB
- 4ZHC
- Type
- protein
- Length
- 517 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neutrophil gelatinase-associated lipocalin
- UniProt
- P80188
- Ligands
- TC2, TH, SO4
- Pockets
- 6 · best druggability 0.56
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 | 168 | 13% helix, 45% strand | P80188 |
| C | Neutrophil gelatinase-associated lipocalin | protein | 174 | 13% 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
- TH · Thorium ion · metal · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 2 copies · chains C
- ACT · Acetate ion · additive · 2 copies · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 303 | 0.56 | 0.76 | 38 | TH, TC2 |
| 2 | 275 | 0.56 | 0.76 | 32 | TH, TC2 |
| 3 | 257 | 0.54 | 0.76 | 33 | TH, TC2 |
| 4 | 226 | 0.49 | 0.74 | 29 | empty |
| 5 | 139 | 0.41 | 0.75 | 27 | ACT |
Interfaces
2 interfaces between chains.
- A–C · 409 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 185 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4ZHC · Siderocalin-mediated recognition and cellular uptake of actinides · 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 4ZHC · PDBe 4ZHC · UniProt P80188
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