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Crystal structure of beta-glycosides-binding protein (W67A) of ABC transporter in an open-liganded state bound to gentiobiose
Analyse Crystal structure of beta-glycosides-binding protein (W67A) of ABC transporter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7C70
- Type
- protein
- Length
- 832 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sugar ABC transporter, periplasmic sugar-binding protein
- UniProt
- Q53W80
- Ligands
- SO2, BGC, CO2, SO4, SO3, PO4
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sugar ABC transporter, periplasmic sugar-binding protein | protein | 417 | 50% helix, 16% strand | Q53W80 |
| B | Sugar ABC transporter, periplasmic sugar-binding protein | protein | 415 | 51% helix, 16% strand | Q53W80 |
Ligands and binding sites
- SO2 · Sulfur dioxide · ligand · 3 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 4 copies · chains A, B
- CO2 · Carbon dioxide · ion · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains B
- SO3 · Sulfite ion · ion · chains A
- PO4 · Phosphate ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- PGO · S-1,2-propanediol · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- IMD · Imidazole · additive · chains 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 466 | 0.78 | 0.86 | 56 | BGC, PGO |
| 2 | 505 | 0.77 | 0.85 | 63 | BGC, PEG |
| 3 | 271 | 0.57 | 0.78 | 35 | empty |
| 4 | 198 | 0.55 | 0.79 | 35 | empty |
| 5 | 124 | 0.49 | 0.80 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1594 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7C70 · Crystal structure of beta-glycosides-binding protein (W67A) of ABC transporter in an… · 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 Q53W80
- Elsewhere: RCSB PDB 7C70 · PDBe 7C70 · UniProt Q53W80
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