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The mutant structure of human siderocalin W79A, R81A, Y106F bound to enterobactin
Analyse The mutant structure of human siderocalin W79A, R81A, Y106F bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3T1D
- Type
- protein
- Length
- 521 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neutrophil gelatinase-associated lipocalin
- UniProt
- P80188
- Ligands
- DBS, TD1, DBH, CL, UNX
- Pockets
- 7 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 43% 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 | 174 | 15% helix, 43% strand | P80188 |
| C | Neutrophil gelatinase-associated lipocalin | protein | 172 | 15% helix, 44% strand | P80188 |
Ligands and binding sites
- DBS · 2-(2,3-dihydroxy-benzoylamino)-3-hydroxy-propionic acid · ligand · 2 copies · chains B, C
- TD1 · O-[(2S)-2-amino-3-hydroxypropanoyl]-N-(2,3-dihydroxybenzoyl)-L-serine · ligand · chains A
- DBH · 2,3-dihydroxy-benzoic acid · ligand · chains B
- CL · Chloride ion · ion · 3 copies · chains A
- UNX · Unknown atom or ion · ion · chains A
- GOL · Glycerol · additive · 7 copies · chains A, B, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 331 | 0.59 | 0.77 | 37 | TD1, UNX |
| 2 | 276 | 0.58 | 0.78 | 30 | DBS, DBH |
| 3 | 299 | 0.58 | 0.77 | 30 | DBS |
| 4 | 251 | 0.58 | 0.79 | 45 | empty |
| 5 | 157 | 0.53 | 0.80 | 25 | empty |
Interfaces
2 interfaces between chains.
- B–C · 554 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 514 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3T1D · The mutant structure of human Siderocalin W79A, R81A, Y106F bound to 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 3T1D · PDBe 3T1D · UniProt P80188
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