MolNFT v1 · #174784 · protein
Crystal structure of beta-glycosides-binding protein (W177X) of ABC transporter in an open-liganded state bound to sophorose
7C6I · Sugar ABC transporter, periplasmic sugar-binding protein: “Crystal structure of beta-glycosides-binding protein (W177X) of ABC transporter in an open-liganded state…”. X-ray diffraction, 4 ligands (SO2, BGC, SO4), 5 pockets (best…
- PDB
- 7C6I
- Type
- protein
- Length
- 837 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, SO4, CO2
- Pockets
- 5 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sugar ABC transporter, periplasmic sugar-binding protein | protein | 420 | 51% helix, 18% strand | Q53W80 |
| B | Sugar ABC transporter, periplasmic sugar-binding protein | protein | 417 | 51% helix, 17% strand | Q53W80 |
Ligands and binding sites
- SO2 · Sulfur dioxide · ligand · chains A
- BGC · beta-D-glucopyranose · sugar · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- CO2 · Carbon dioxide · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains A
- BU2 · 1,3-butanediol · additive · chains A, B
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 | 991 | 0.86 | 0.87 | 123 | BGC |
| 2 | 386 | 0.62 | 0.77 | 56 | BGC |
| 3 | 151 | 0.42 | 0.74 | 21 | empty |
| 4 | 55 | 0.37 | 0.80 | 14 | empty |
| 5 | 70 | 0.32 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1325 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7C6I · Crystal structure of beta-glycosides-binding protein (W177X) 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 7C6I · PDBe 7C6I · UniProt Q53W80
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