Research workbench
Crystal structure of lpqy from mycobacterium thermoresistible in complex with trehalose
Analyse Crystal structure of lpqy from mycobacterium thermoresistible in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7APE
- Type
- protein
- Length
- 870 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipoprotein (sugar-binding) lpqy
- UniProt
- A0A100XFZ4
- Ligands
- GLC
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lipoprotein (sugar-binding) lpqy | protein | 435 | 47% helix, 15% strand | A0A100XFZ4 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B
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 | 1146 | 0.82 | 0.83 | 117 | empty |
| 2 | 507 | 0.76 | 0.83 | 55 | GLC |
| 3 | 371 | 0.74 | 0.85 | 38 | GLC |
| 4 | 180 | 0.47 | 0.76 | 28 | empty |
| 5 | 122 | 0.42 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1375 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7APE · Crystal structure of LpqY from Mycobacterium thermoresistible in complex with trehalose · 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 A0A100XFZ4
- Elsewhere: RCSB PDB 7APE · PDBe 7APE · UniProt A0A100XFZ4
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