MolNFT v1 · #158811 · protein
PYOCHELIN
6O5D · Neutrophil gelatinase-associated lipocalin: “PYOCHELIN”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.57). MolNFT v1 #158811 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6O5D
- Type
- protein
- Length
- 514 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neutrophil gelatinase-associated lipocalin
- UniProt
- P80188
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.57
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 | 174 | 15% helix, 43% strand | P80188 |
| B | Neutrophil gelatinase-associated lipocalin | protein | 167 | 16% helix, 45% strand | P80188 |
| C | Neutrophil gelatinase-associated lipocalin | protein | 173 | 15% helix, 43% strand | P80188 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C
- GOL · Glycerol · additive · 2 copies · chains C, A
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 | 259 | 0.57 | 0.77 | 39 | SO4 |
| 2 | 183 | 0.57 | 0.80 | 29 | SO4 |
| 3 | 174 | 0.56 | 0.80 | 30 | SO4 |
| 4 | 129 | 0.40 | 0.75 | 26 | empty |
| 5 | 59 | 0.29 | 0.75 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–C · 427 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 115 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6O5D · PYOCHELIN · 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 6O5D · PDBe 6O5D · UniProt P80188
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