MolNFT v1 · #174782 · protein
Crystal structure of beta-glycosides-binding protein (W177X) of ABC transporter in an open-liganded state bound to gentiobiose
7C6G · 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, 5 ligands (BGC, CL, SO4), 4 pockets (best…
- PDB
- 7C6G
- Type
- protein
- Length
- 835 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
- BGC, CL, SO4, CO2, SO3
- Pockets
- 4 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sugar ABC transporter, periplasmic sugar-binding protein | protein | 420 | 51% helix, 17% strand | Q53W80 |
| B | Sugar ABC transporter, periplasmic sugar-binding protein | protein | 415 | 52% helix, 17% strand | Q53W80 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 4 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- CO2 · Carbon dioxide · ion · chains B
- SO3 · Sulfite ion · ion · chains B
- PGO · S-1,2-propanediol · additive · chains A
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 999 | 0.86 | 0.87 | 120 | BGC, CL |
| 2 | 408 | 0.63 | 0.77 | 60 | BGC |
| 3 | 123 | 0.40 | 0.74 | 18 | empty |
| 4 | 75 | 0.33 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1475 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7C6G · 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 7C6G · PDBe 7C6G · UniProt Q53W80
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