MolNFT v1 · #112310 · protein
Siderocalin-mediated recognition and cellular uptake of actinides
4ZHH · Neutrophil gelatinase-associated lipocalin: “Siderocalin-mediated recognition and cellular uptake of actinides”. X-ray diffraction, 4 ligands (4OL, SM, CL), 12 pockets (best druggability 0.80). MolNFT v1 #112310 on GenesisL1: 3D…
- PDB
- 4ZHH
- Type
- protein
- Length
- 1,054 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neutrophil gelatinase-associated lipocalin
- UniProt
- P80188
- Ligands
- 4OL, SM, CL, SO4
- Pockets
- 12 · best druggability 0.80
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 | 177 | 12% helix, 42% strand | P80188 |
| B, C, F | Neutrophil gelatinase-associated lipocalin | protein | 175 | 13% helix, 43% strand | P80188 |
| D, E | Neutrophil gelatinase-associated lipocalin | protein | 176 | 13% helix, 43% strand | P80188 |
Ligands and binding sites
- 4OL · N,N'-butane-1,4-diylbis[1-hydroxy-N-(3-{[(1-hydroxy-6-oxo-1,6-dihydropyridin-2-yl)carbonyl]amino}propyl)-6-oxo-1,6-dihydropyridine-2-carboxamide] · ligand · 6 copies · chains A, B, C, D, E, F
- SM · Samarium (III) ion · metal · 6 copies · chains A, B, D
- CL · Chloride ion · ion · 8 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, D, C, E, F
- GOL · Glycerol · additive · 5 copies · chains A, B, D, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1077 | 0.80 | 0.82 | 100 | GOL |
| 2 | 626 | 0.75 | 0.82 | 61 | empty |
| 3 | 240 | 0.53 | 0.76 | 26 | SM, 4OL, CL |
| 4 | 198 | 0.53 | 0.77 | 29 | SM, 4OL, CL |
| 5 | 203 | 0.52 | 0.77 | 26 | SM, 4OL, CL |
Interfaces
8 interfaces between chains.
- A–B · 512 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 481 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 383 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 376 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 351 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4ZHH · 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 4ZHH · PDBe 4ZHH · UniProt P80188
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