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Crystal structure of siderocalin (ngal, lipocalin 2) complexed with carboxymycobactin S
Analyse Crystal structure of siderocalin (ngal, lipocalin 2) complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1X89
- 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
- CM1
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neutrophil gelatinase-associated lipocalin | protein | 174 | 14% helix, 43% strand | P80188 |
| B | Neutrophil gelatinase-associated lipocalin | protein | 171 | 15% helix, 44% strand | P80188 |
| C | Neutrophil gelatinase-associated lipocalin | protein | 173 | 15% helix, 43% strand | P80188 |
Ligands and binding sites
- CM1 · Carboxymycobactin S · ligand · 3 copies · chains A, B, 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 | 377 | 0.66 | 0.79 | 32 | CM1 |
| 2 | 396 | 0.65 | 0.78 | 35 | CM1 |
| 3 | 292 | 0.61 | 0.79 | 33 | CM1 |
| 4 | 212 | 0.47 | 0.74 | 35 | empty |
| 5 | 125 | 0.39 | 0.74 | 26 | empty |
Interfaces
2 interfaces between chains.
- A–C · 403 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 112 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1X89 · Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with Carboxymycobactin S · 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 1X89 · PDBe 1X89 · UniProt P80188
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