Research workbench
Siderocalin-mediated recognition and cellular uptake of actinides
Analyse Siderocalin-mediated recognition and cellular uptake of actinides in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZHF
- Type
- protein
- Length
- 1,055 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neutrophil gelatinase-associated lipocalin
- UniProt
- P80188
- Ligands
- 4OL, ZCM, SO4
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | 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 |
| E | Neutrophil gelatinase-associated lipocalin | protein | 176 | 15% 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
- ZCM · Curium ion · metal · 6 copies · chains A, B, D
- SO4 · Sulfate ion · ion · 10 copies · chains A, B, D, C, E, F
- GOL · Glycerol · additive · 4 copies · chains B, A, C, 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 686 | 0.77 | 0.82 | 62 | empty |
| 2 | 615 | 0.75 | 0.82 | 63 | empty |
| 3 | 310 | 0.64 | 0.81 | 38 | empty |
| 4 | 379 | 0.56 | 0.74 | 49 | empty |
| 5 | 213 | 0.52 | 0.76 | 26 | ZCM, 4OL, SO4 |
Interfaces
8 interfaces between chains.
- A–B · 512 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 508 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 378 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 375 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 365 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4ZHF · 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 4ZHF · PDBe 4ZHF · UniProt P80188
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