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Crystal structure of siderocalin (ngal, lipocalin 2) K134A mutant complexed with ferric enterobactin
Analyse Crystal structure of siderocalin (ngal, lipocalin 2) K134A mutant complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3I0A
- 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
- 3ET, 2DS, DBH, MCJ, FE, SO4
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 42% 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 | 164 | 11% helix, 40% strand | P80188 |
| C | Neutrophil gelatinase-associated lipocalin | protein | 176 | 11% helix, 43% strand | P80188 |
Ligands and binding sites
- 3ET · O-[(2R)-2-amino-3-(D-seryloxy)propanoyl]-N-[(2,3-dihydroxyphenyl)carbonyl]-L-serine · ligand · chains A
- 2DS · N-[(2,3-dihydroxyphenyl)carbonyl]-O-[(2R)-2-{[(2,3-dihydroxyphenyl)carbonyl]amino}-3-hydroxypropanoyl]-L-serine · ligand · chains A
- DBH · 2,3-dihydroxy-benzoic acid · ligand · chains B
- MCJ · N-[(2,3-dihydroxyphenyl)carbonyl]-O-[(2S)-2-{[(2,3-dihydroxyphenyl)carbonyl]amino}-3-({N-[(2,3-dihydroxyphenyl)carbonyl]-L-seryl}oxy)propanoyl]-D-serine · ligand · chains C
- FE · Fe (III) ion · metal · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
- GOL · Glycerol · additive · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 329 | 0.63 | 0.79 | 32 | FE, MCJ |
| 2 | 311 | 0.62 | 0.78 | 39 | FE, DBH |
| 3 | 318 | 0.62 | 0.78 | 35 | FE, 3ET, 2DS |
| 4 | 200 | 0.45 | 0.73 | 23 | empty |
| 5 | 154 | 0.43 | 0.75 | 28 | empty |
Interfaces
2 interfaces between chains.
- A–C · 375 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 86 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3I0A · Crystal structure of Siderocalin (NGAL, Lipocalin 2) K134A mutant complexed with Ferric… · 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 3I0A · PDBe 3I0A · UniProt P80188
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