MolNFT v1 · #124545 · protein
Long-sought stabilization of BERKELIUM(IV) in solution: an anomaly within the heavy actinide series
5KIC · Neutrophil gelatinase-associated lipocalin: “Long-sought stabilization of BERKELIUM(IV) in solution: an anomaly within the heavy actinide series”. X-ray diffraction, 4 ligands (4OL, CF, CL), 7 pockets (best druggability 0.51).…
- PDB
- 5KIC
- Type
- protein
- Length
- 523 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neutrophil gelatinase-associated lipocalin
- UniProt
- P80188
- Ligands
- 4OL, CF, CL, SO4
- Pockets
- 7 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neutrophil gelatinase-associated lipocalin | protein | 173 | 15% helix, 43% strand | P80188 |
| B, C | Neutrophil gelatinase-associated lipocalin | protein | 175 | 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 · 3 copies · chains A, B, C
- CF · Californium ion · metal · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 3 copies · chains C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 201 | 0.51 | 0.76 | 28 | CF, 4OL, CL |
| 2 | 241 | 0.50 | 0.75 | 29 | empty |
| 3 | 170 | 0.49 | 0.77 | 25 | CF, 4OL, CL |
| 4 | 172 | 0.49 | 0.76 | 25 | CF, 4OL, CL |
| 5 | 167 | 0.47 | 0.76 | 32 | empty |
Interfaces
2 interfaces between chains.
- A–C · 385 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 311 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5KIC · Long-sought stabilization of berkelium(IV) in solution: An anomaly within the heavy… · 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 5KIC · PDBe 5KIC · UniProt P80188
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