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Crystal structure of siderocalin (ngal, lipocalin 2) complexed with trencam-3,2-hopo, a cepabactin analogue
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
- 1X71
- Type
- protein
- Length
- 520 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neutrophil gelatinase-associated lipocalin
- UniProt
- P80188
- Ligands
- DB1, FE
- Pockets
- 6 · best druggability 0.51
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 | 175 | 14% helix, 43% strand | P80188 |
| B | Neutrophil gelatinase-associated lipocalin | protein | 171 | 15% helix, 44% strand | P80188 |
| C | Neutrophil gelatinase-associated lipocalin | protein | 174 | 15% helix, 43% strand | P80188 |
Ligands and binding sites
- DB1 · 2,3-dihydroxybenzamide · ligand · 5 copies · chains A, B, C
- FE · Fe (III) ion · metal · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 225 | 0.51 | 0.75 | 27 | FE, DB1 |
| 2 | 196 | 0.48 | 0.75 | 28 | FE, DB1 |
| 3 | 214 | 0.46 | 0.74 | 35 | empty |
| 4 | 148 | 0.46 | 0.76 | 26 | FE, DB1 |
| 5 | 126 | 0.39 | 0.75 | 24 | empty |
Interfaces
2 interfaces between chains.
- A–C · 397 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 140 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1X71 · Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with TRENCAM-3,2-HOPO, a… · 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 1X71 · PDBe 1X71 · UniProt P80188
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