MolNFT v2 · #214001 · protein
Crystal structure of Mycobacterium tuberculosis LpqY in complex with trehalose analogue YB-04
8JAA · Trehalose-binding lipoprotein LpqY: “Crystal structure of Mycobacterium tuberculosis LpqY in complex with trehalose analogue YB-04”. X-ray diffraction at 1.7, 2 ligands (TY6, SO4), 5 pockets (best druggability 0.77). MolNFT v2…
- PDB
- 8JAA
- Type
- protein
- Length
- 433 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.7
- Source
- Mycobacterium tuberculosis H37Rv
- Molecule
- Trehalose-binding lipoprotein LpqY
- UniProt
- P9WGU9
- Ligands
- TY6, SO4
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · resolution 1.7 · 1 distinct chain · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trehalose-binding lipoprotein LpqY | protein | 433 | 48% helix, 16% strand | P9WGU9 |
Ligands and binding sites
- TY6 · (2~{S},3~{R},4~{S},5~{S},6~{S})-6-[(2-azanylhydrazinyl)methyl]oxane-2,3,4,5-tetrol · sugar · 2 copies · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 745 | 0.77 | 0.81 | 70 | SO4, TY6 |
| 2 | 120 | 0.70 | 0.91 | 29 | empty |
| 3 | 50 | 0.43 | 0.84 | 16 | empty |
| 4 | 55 | 0.28 | 0.74 | 21 | empty |
| 5 | 60 | 0.27 | 0.73 | 16 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- P9WGU9 · AlphaFold monomer V2.0 prediction for trehalose-binding lipoprotein lpqy (P9WGU9) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P9WGU9
- Elsewhere: RCSB PDB 8JAA · PDBe 8JAA · UniProt P9WGU9
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