Research workbench
Crystal structure of neutrophil gelatinase-associated lipocalin (C87S mutant) in complex with europium and the siderophore analog TREN(CAM)(1,2-HOPO)2
Analyse Crystal structure of neutrophil gelatinase-associated lipocalin (C87S mutant)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TF6
- 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
- DBH, EU, CL, SO4
- Pockets
- 6 · best druggability 0.51
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 | 176 | 13% helix, 43% strand | P80188 |
| B | Neutrophil gelatinase-associated lipocalin | protein | 171 | 13% helix, 44% strand | P80188 |
| C | Neutrophil gelatinase-associated lipocalin | protein | 173 | 13% helix, 43% strand | P80188 |
Ligands and binding sites
- DBH · 2,3-dihydroxy-benzoic acid · ligand · 3 copies · chains A, B, C
- EU · Europium ion · metal · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 5 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 4 copies · chains A, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 194 | 0.51 | 0.76 | 23 | EU, DBH |
| 2 | 187 | 0.50 | 0.76 | 27 | EU, DBH, SO4 |
| 3 | 177 | 0.50 | 0.76 | 28 | EU, DBH, SO4 |
| 4 | 118 | 0.38 | 0.75 | 28 | empty |
| 5 | 86 | 0.31 | 0.72 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–C · 426 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 77 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3TF6 · Crystal structure of Neutrophil gelatinase-associated lipocalin (C87S mutant) in complex… · 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 3TF6 · PDBe 3TF6 · UniProt P80188
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