MolNFT v1 · #124523 · protein
Tightening the recognition of tetravalent zr and th complexes by the siderophore-binding mammalian protein siderocalin for theranostic applications
5KHP · Neutrophil gelatinase-associated lipocalin: “Tightening the recognition of tetravalent zr and th complexes by the siderophore-binding mammalian protein…”. X-ray diffraction, 3 ligands (7K9, ZR, SO4), 7 pockets (best druggability…
- PDB
- 5KHP
- 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
- 7K9, ZR, SO4
- Pockets
- 7 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Neutrophil gelatinase-associated lipocalin | protein | 173 | 13% helix, 43% strand | P80188 |
| B | Neutrophil gelatinase-associated lipocalin | protein | 171 | 13% helix, 44% 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
- ZR · Zirconium ion · metal · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 8 copies · chains A, C
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 176 | 0.57 | 0.81 | 31 | ZR, 7K9 |
| 2 | 232 | 0.57 | 0.78 | 34 | ZR, 7K9 |
| 3 | 222 | 0.56 | 0.78 | 36 | ZR, 7K9 |
| 4 | 114 | 0.37 | 0.73 | 22 | empty |
| 5 | 84 | 0.35 | 0.75 | 21 | empty |
Interfaces
2 interfaces between chains.
- A–C · 418 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 238 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5KHP · Tightening the Recognition of Tetravalent Zr and Th Complexes by the Siderophore-Binding… · 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 5KHP · PDBe 5KHP · UniProt P80188
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