Research workbench
Crystal structure of siderocalin (ngal, lipocalin 2) complexed with apo enterobactin
Analyse Crystal structure of siderocalin (ngal, lipocalin 2) complexed with apo… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K3L
- Type
- protein
- Length
- 504 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neutrophil gelatinase-associated lipocalin
- UniProt
- P80188
- Ligands
- DBH, DBS, MCK, NA, SO4, CL
- Pockets
- 10 · best druggability 0.73
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 | 175 | 15% helix, 43% strand | P80188 |
| B | Neutrophil gelatinase-associated lipocalin | protein | 154 | 10% helix, 39% strand | P80188 |
| C | Neutrophil gelatinase-associated lipocalin | protein | 175 | 15% helix, 43% strand | P80188 |
Ligands and binding sites
- DBH · 2,3-dihydroxy-benzoic acid · ligand · 2 copies · chains A
- DBS · 2-(2,3-dihydroxy-benzoylamino)-3-hydroxy-propionic acid · ligand · chains A
- MCK · N-[(2,3-dihydroxyphenyl)carbonyl]-O-[(2S)-2-{[(2,3-dihydroxyphenyl)carbonyl]amino}-3-(L-seryloxy)propanoyl]-L-serine · ligand · chains C
- NA · Sodium ion · metal · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · chains A
- CL · Chloride ion · ion · chains C
- GOL · Glycerol · additive · 7 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 526 | 0.73 | 0.81 | 69 | empty |
| 2 | 152 | 0.58 | 0.83 | 29 | empty |
| 3 | 196 | 0.50 | 0.76 | 26 | DBS, DBH, NA |
| 4 | 195 | 0.50 | 0.76 | 24 | MCK |
| 5 | 173 | 0.49 | 0.77 | 32 | empty |
Interfaces
2 interfaces between chains.
- A–C · 406 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 54 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3K3L · Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with apo Enterobactin · 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 3K3L · PDBe 3K3L · UniProt P80188
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