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Crystal structure of siderocalin (ngal, lipocalin 2) K125A mutant complexed with ferric enterobactin
Analyse Crystal structure of siderocalin (ngal, lipocalin 2) K125A mutant complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CMP
- Type
- protein
- Length
- 516 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neutrophil gelatinase-associated lipocalin
- UniProt
- P80188
- Ligands
- EB4, DBH, NA, FE, SO4
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neutrophil gelatinase-associated lipocalin | protein | 174 | 13% helix, 43% strand | P80188 |
| B | Neutrophil gelatinase-associated lipocalin | protein | 168 | 11% helix, 42% strand | P80188 |
| C | Neutrophil gelatinase-associated lipocalin | protein | 174 | 15% helix, 43% strand | P80188 |
Ligands and binding sites
- EB4 · N,N',N''-[(3S,7S,11S)-2,6,10-trioxo-1,5,9-trioxacyclododecane-3,7,11-triyl]tris(2,3-dihydroxybenzamide) · ligand · 2 copies · chains A, C
- DBH · 2,3-dihydroxy-benzoic acid · ligand · 2 copies · chains B
- NA · Sodium ion · metal · 7 copies · chains A, B, C
- FE · Fe (III) ion · metal · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 3 copies · chains A, C
- GOL · Glycerol · additive · 3 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 354 | 0.68 | 0.81 | 48 | FE, NA, DBH |
| 2 | 273 | 0.55 | 0.76 | 28 | FE, NA, EB4 |
| 3 | 240 | 0.52 | 0.75 | 25 | FE, NA, SO4, EB4 |
| 4 | 140 | 0.40 | 0.74 | 26 | empty |
| 5 | 85 | 0.37 | 0.76 | 25 | empty |
Interfaces
2 interfaces between chains.
- A–C · 410 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 10 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3CMP · Crystal structure of Siderocalin (NGAL, Lipocalin 2) K125A 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 3CMP · PDBe 3CMP · UniProt P80188
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