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
- 4ZHD
- Type
- protein
- Length
- 521 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neutrophil gelatinase-associated lipocalin
- UniProt
- P80188
- Ligands
- 4OZ, 4PU, SO4
- Pockets
- 6 · best druggability 0.56
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 | 174 | 13% helix, 43% strand | P80188 |
| B | Neutrophil gelatinase-associated lipocalin | protein | 172 | 15% helix, 44% strand | P80188 |
| C | Neutrophil gelatinase-associated lipocalin | protein | 175 | 13% helix, 43% strand | P80188 |
Ligands and binding sites
- 4OZ · methyl N-(2,3-dihydroxybenzoyl)-O-formyl-L-serinate · ligand · 3 copies · chains A, B, C
- 4PU · Plutonium ion · metal · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 2 copies · chains C
- GOL · Glycerol · 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 | 276 | 0.56 | 0.76 | 30 | 4PU, 4OZ |
| 2 | 286 | 0.55 | 0.76 | 27 | 4PU, 4OZ |
| 3 | 295 | 0.55 | 0.75 | 30 | 4PU, 4OZ |
| 4 | 235 | 0.48 | 0.73 | 28 | empty |
| 5 | 124 | 0.40 | 0.75 | 25 | empty |
Interfaces
2 interfaces between chains.
- A–C · 413 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 179 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4ZHD · Siderocalin-mediated recognition and cellular uptake of actinides · the same entry in another collection · chain C against C, TM-score 1.00
- P80188 · AlphaFold monomer V2.0 prediction for neutrophil gelatinase- associated lipocalin (P80188) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 4ZHD · PDBe 4ZHD · UniProt P80188
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