MolNFT v1 · #174797 · protein
Crystal structure of beta-glycosides-binding protein (W177X) of ABC transporter in a closed state bound to laminaritriose (form II)
7C6V · Sugar ABC transporter, periplasmic sugar-binding protein: “Crystal structure of beta-glycosides-binding protein (W177X) of ABC transporter in a closed state bound to…”. X-ray diffraction, 4 ligands (BGC, SO4, CL), 7 pockets (best…
- PDB
- 7C6V
- Type
- protein
- Length
- 1,238 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sugar ABC transporter, periplasmic sugar-binding protein
- UniProt
- Q53W80
- Ligands
- BGC, SO4, CL, SO3
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sugar ABC transporter, periplasmic sugar-binding protein | protein | 413 | 49% helix, 18% strand | Q53W80 |
| B | Sugar ABC transporter, periplasmic sugar-binding protein | protein | 413 | 51% helix, 17% strand | Q53W80 |
| C | Sugar ABC transporter, periplasmic sugar-binding protein | protein | 412 | 49% helix, 17% strand | Q53W80 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 9 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C
- CL · Chloride ion · ion · 3 copies · chains A, B, C
- SO3 · Sulfite ion · ion · chains C
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1015 | 0.77 | 0.79 | 77 | empty |
| 2 | 1127 | 0.74 | 0.77 | 84 | CL |
| 3 | 541 | 0.71 | 0.80 | 52 | BGC, CL, SO4 |
| 4 | 446 | 0.71 | 0.81 | 38 | BGC, SO4 |
| 5 | 660 | 0.70 | 0.78 | 61 | empty |
Interfaces
2 interfaces between chains.
- A–B · 846 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 377 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7C6V · Crystal structure of beta-glycosides-binding protein (W177X) of ABC transporter in a… · 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 7C6V · PDBe 7C6V · UniProt Q53W80
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