MolNFT v1 · #161712 · protein
A tetrahedral boronic acid diester formed by a non-natural amino acid in the ligand pocket of an engineered lipocalin
6QMU · Neutrophil gelatinase-associated lipocalin: “A tetrahedral boronic acid diester formed by a non-natural amino acid in the ligand pocket of an engineered…”. X-ray diffraction, 1 ligand (ZCQ), 3 pockets (best druggability 0.63).…
- PDB
- 6QMU
- Type
- protein
- Length
- 368 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neutrophil gelatinase-associated lipocalin
- UniProt
- P80188
- Ligands
- ZCQ
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 12% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Neutrophil gelatinase-associated lipocalin | protein | 184 | 12% helix, 41% strand | P80188 |
Ligands and binding sites
- ZCQ · 3-nitrophenol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 413 | 0.63 | 0.77 | 54 | empty |
| 2 | 318 | 0.57 | 0.76 | 37 | ZCQ |
| 3 | 167 | 0.50 | 0.77 | 30 | ZCQ |
Interfaces
1 interface between chains.
- A–B · 421 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 disulfide, 2 modified (covalent ligand, disulfide, nonstandard).
Compared structures
- 6QMU · A tetrahedral boronic acid diester formed by a non-natural amino acid in the ligand… · 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 6QMU · PDBe 6QMU · UniProt P80188
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