MolNFT v1 · #27075 · protein
Crystal structure of siderocalin (ngal, lipocalin 2) complexed with carboxymycobactin T
1X8U · Neutrophil gelatinase-associated lipocalin: “Crystal structure of siderocalin (ngal, lipocalin 2) complexed with carboxymycobactin T”. X-ray diffraction, 1 ligand (CM2), 6 pockets (best druggability 0.65). MolNFT v1 #27075 on…
- PDB
- 1X8U
- Type
- protein
- Length
- 517 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neutrophil gelatinase-associated lipocalin
- UniProt
- P80188
- Ligands
- CM2
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 44% 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 | 169 | 15% helix, 44% strand | P80188 |
| C | Neutrophil gelatinase-associated lipocalin | protein | 173 | 15% helix, 43% strand | P80188 |
Ligands and binding sites
- CM2 · Carboxymycobactin T · 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 | 409 | 0.65 | 0.78 | 37 | CM2 |
| 2 | 308 | 0.63 | 0.79 | 30 | CM2 |
| 3 | 328 | 0.63 | 0.78 | 30 | CM2 |
| 4 | 121 | 0.38 | 0.74 | 24 | empty |
| 5 | 125 | 0.37 | 0.73 | 21 | empty |
Interfaces
2 interfaces between chains.
- A–C · 383 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 121 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1X8U · Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with Carboxymycobactin T · 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 1X8U · PDBe 1X8U · UniProt P80188
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