Research workbench
Crystal structure of siderocalin (ngal, lipocalin 2) W79A-R81A complexed with ferric enterobactin
Analyse Crystal structure of siderocalin (ngal, lipocalin 2) W79A-R81A complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BY0
- Type
- protein
- Length
- 519 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neutrophil gelatinase-associated lipocalin
- UniProt
- P80188
- Ligands
- DBH, DBS, FE, SO4
- Pockets
- 6 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 14% 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 | 171 | 15% helix, 42% strand | P80188 |
| C | Neutrophil gelatinase-associated lipocalin | protein | 174 | 15% helix, 43% strand | P80188 |
Ligands and binding sites
- DBH · 2,3-dihydroxy-benzoic acid · ligand · 4 copies · chains A, B, C
- DBS · 2-(2,3-dihydroxy-benzoylamino)-3-hydroxy-propionic acid · ligand · 3 copies · chains A, C
- FE · Fe (III) ion · metal · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
- GOL · Glycerol · additive · 3 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 316 | 0.58 | 0.76 | 36 | FE, DBS, DBH |
| 2 | 231 | 0.56 | 0.77 | 28 | FE, DBH |
| 3 | 244 | 0.54 | 0.77 | 30 | FE, DBS, DBH |
| 4 | 298 | 0.54 | 0.75 | 38 | empty |
| 5 | 91 | 0.35 | 0.75 | 22 | empty |
Interfaces
2 interfaces between chains.
- A–C · 395 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 289 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3BY0 · Crystal structure of Siderocalin (NGAL, Lipocalin 2) W79A-R81A complexed with Ferric… · 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 3BY0 · PDBe 3BY0 · UniProt P80188
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.