MolNFT v1 · #174773 · protein
Crystal structure of beta-glycosides-binding protein of ABC transporter in a closed state bound to cellobiose
7C66 · Sugar ABC transporter, periplasmic sugar-binding protein: “Crystal structure of beta-glycosides-binding protein of ABC transporter in a closed state bound to cellobiose”. X-ray diffraction, 5 ligands (SO2, GLC, BGC), 7 pockets (best…
- PDB
- 7C66
- Type
- protein
- Length
- 836 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, GLC, BGC, CL, SO3
- Pockets
- 7 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Sugar ABC transporter, periplasmic sugar-binding protein | protein | 418 | 52% helix, 16% strand | Q53W80 |
Ligands and binding sites
- SO2 · Sulfur dioxide · ligand · chains B
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- SO3 · Sulfite ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 971 | 0.89 | 0.90 | 116 | GLC, BGC, CL, EDO |
| 2 | 545 | 0.68 | 0.78 | 57 | empty |
| 3 | 73 | 0.39 | 0.78 | 13 | empty |
| 4 | 50 | 0.36 | 0.80 | 14 | empty |
| 5 | 88 | 0.35 | 0.75 | 15 | SO3 |
Interfaces
1 interface between chains.
- A–B · 1771 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7C66 · Crystal structure of beta-glycosides-binding protein of ABC transporter in a closed state… · 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 7C66 · PDBe 7C66 · UniProt Q53W80
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