Research workbench
Crystal structure of siderocalin (ngal, lipocalin 2) complexed with fe-bishacam
Analyse Crystal structure of siderocalin (ngal, lipocalin 2) complexed with fe-bishacam in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HWE
- Type
- protein
- Length
- 518 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neutrophil gelatinase-associated lipocalin
- UniProt
- P80188
- Ligands
- RKS, NA, FE, SO4
- Pockets
- 6 · best druggability 0.55
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 | 174 | 13% helix, 44% strand | P80188 |
| B | Neutrophil gelatinase-associated lipocalin | protein | 170 | 14% helix, 44% strand | P80188 |
Ligands and binding sites
- RKS · methyl N~6~-acetyl-N~2~-[(2,3-dihydroxyphenyl)carbonyl]-N~6~-hydroxy-D-lysyl-N~6~-acetyl-N~6~-hydroxy-L-lysinate · ligand · 6 copies · chains A, B, C
- NA · Sodium ion · metal · 4 copies · chains A, C
- FE · Fe (III) ion · metal · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 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 | 257 | 0.55 | 0.76 | 38 | FE, RKS |
| 2 | 197 | 0.54 | 0.78 | 31 | FE, RKS, SO4 |
| 3 | 216 | 0.52 | 0.76 | 39 | FE, RKS |
| 4 | 104 | 0.34 | 0.73 | 24 | empty |
| 5 | 76 | 0.32 | 0.75 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–C · 418 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 89 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3HWE · Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with Fe-BisHaCam · 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 3HWE · PDBe 3HWE · UniProt P80188
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