Research workbench
Tightening the recognition of tetravalent zr and th complexes by the siderophore-binding mammalian protein siderocalin for theranostic applications
Analyse Tightening the recognition of tetravalent zr and th complexes by the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KID
- Type
- protein
- Length
- 516 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neutrophil gelatinase-associated lipocalin
- UniProt
- P80188
- Ligands
- 7K9, TH, SO4, CL
- Pockets
- 6 · best druggability 0.53
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neutrophil gelatinase-associated lipocalin | protein | 173 | 15% helix, 43% strand | P80188 |
| B | Neutrophil gelatinase-associated lipocalin | protein | 169 | 15% helix, 44% strand | P80188 |
| C | Neutrophil gelatinase-associated lipocalin | protein | 174 | 15% helix, 43% strand | P80188 |
Ligands and binding sites
- 7K9 · N,N'-(butane-1,4-diyl)bis(N-{3-[(2,3-dihydroxybenzene-1-carbonyl)amino]propyl}-2,3-dihydroxybenzamide) · ligand · 3 copies · chains A, B, C
- TH · Thorium ion · metal · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 3 copies · chains A, C
- CL · Chloride ion · ion · 2 copies · chains A, 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 291 | 0.53 | 0.75 | 52 | TH, 7K9, CL |
| 2 | 220 | 0.50 | 0.75 | 26 | TH, 7K9, CL |
| 3 | 203 | 0.49 | 0.75 | 24 | TH, 7K9 |
| 4 | 113 | 0.38 | 0.75 | 19 | empty |
| 5 | 73 | 0.33 | 0.76 | 17 | empty |
Interfaces
2 interfaces between chains.
- A–C · 420 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 219 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5KID · Tightening the Recognition of Tetravalent Zr and Th Complexes by the Siderophore-Binding… · the same entry in another collection · chain B against B, 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 5KID · PDBe 5KID · UniProt P80188
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