Research workbench
The crystal structure of the W145A variant of tpmglb-2 (TP0684) with bound glucose
Analyse The crystal structure of the W145A variant of tpmglb-2 (TP0684) with bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BGC
- Type
- protein
- Length
- 736 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GLUCOSE/GALACTOSE-binding lipoprotein
- UniProt
- Q08255
- Ligands
- BGC, CA
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GLUCOSE/GALACTOSE-binding lipoprotein | protein | 364 | 36% helix, 23% strand | Q08255 |
| B | GLUCOSE/GALACTOSE-binding lipoprotein | protein | 372 | 35% helix, 22% strand | Q08255 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
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 | 713 | 0.74 | 0.80 | 54 | empty |
| 2 | 136 | 0.71 | 0.91 | 27 | BGC, EDO |
| 3 | 193 | 0.68 | 0.87 | 38 | BGC, EDO |
| 4 | 384 | 0.63 | 0.78 | 50 | empty |
| 5 | 192 | 0.56 | 0.80 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 624 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6BGC · The crystal structure of the W145A variant of TpMglB-2 (Tp0684) with bound glucose · the same entry in another collection · chain A against A, TM-score 1.00
- Q08255 · AlphaFold monomer V2.0 prediction for GLUCOSE/GALACTOSE-binding lipoprotein (Q08255) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q08255
- Elsewhere: RCSB PDB 6BGC · PDBe 6BGC · UniProt Q08255
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