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Crystal structure of beta-glycosides-binding protein (W177X) of ABC transporter in an open-liganded state bound to laminaribiose
Analyse Crystal structure of beta-glycosides-binding protein (W177X) 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
- 7C6H
- 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
- BGC, CL, SO4
- Pockets
- 6 · best druggability 0.82
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, 17% strand | Q53W80 |
| B | Sugar ABC transporter, periplasmic sugar-binding protein | protein | 417 | 52% helix, 17% strand | Q53W80 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 4 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
- ACT · Acetate ion · additive · chains A
- PGO · S-1,2-propanediol · additive · chains B
- PEG · Di(hydroxyethyl)ether · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1016 | 0.82 | 0.83 | 99 | BGC, SO4 |
| 2 | 622 | 0.79 | 0.84 | 71 | EDO, CL |
| 3 | 373 | 0.58 | 0.75 | 41 | BGC, EDO |
| 4 | 143 | 0.42 | 0.74 | 23 | empty |
| 5 | 82 | 0.39 | 0.78 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1402 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7C6H · 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 7C6H · PDBe 7C6H · UniProt Q53W80
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