Research workbench
Petrobactin-binding engineered lipocalin in complex with gallium- petrobactin
Analyse Petrobactin-binding engineered lipocalin in complex with gallium- petrobactin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GR0
- Type
- protein
- Length
- 506 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neutrophil gelatinase-associated lipocalin
- UniProt
- P80188
- Ligands
- F8W, GA
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neutrophil gelatinase-associated lipocalin | protein | 173 | 13% helix, 42% strand | P80188 |
| B | Neutrophil gelatinase-associated lipocalin | protein | 167 | 13% helix, 44% strand | P80188 |
| C | Neutrophil gelatinase-associated lipocalin | protein | 166 | 13% helix, 44% strand | P80188 |
Ligands and binding sites
- F8W · 4-[4-[3-[[3,4-bis(oxidanyl) phenyl]carbonylamino]propylamino]butylamino]-2-[2-[4-[3-[[3,4-bis(oxidanyl) phenyl]carbonylamino]propylamino]butylamino]-2-oxidanylidene-ethyl]-2-oxidanyl-4-oxidanylidene-butanoic acid · ligand · 6 copies · chains A, B, C
- GA · Gallium (III) ion · metal · 7 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 964 | 0.80 | 0.82 | 50 | empty |
| 2 | 323 | 0.56 | 0.75 | 36 | F8W, GA |
| 3 | 245 | 0.53 | 0.76 | 27 | F8W, GA |
| 4 | 212 | 0.51 | 0.76 | 30 | F8W, GA |
| 5 | 75 | 0.44 | 0.81 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 601 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 590 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 493 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6GR0 · Petrobactin-binding engineered lipocalin in complex with gallium-petrobactin · 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 6GR0 · PDBe 6GR0 · UniProt P80188
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