Research workbench
B. thetaiotaomicron susd with beta-cyclodextrin
Analyse B. thetaiotaomicron susd with beta-cyclodextrin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CK8
- Type
- protein
- Length
- 1,002 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Susd
- UniProt
- Q8A1G2
- Ligands
- GLC, CA
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Susd | protein | 501 | 45% helix, 6% strand | Q8A1G2 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 14 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 961 | 0.71 | 0.75 | 87 | empty |
| 2 | 147 | 0.46 | 0.76 | 24 | empty |
| 3 | 126 | 0.43 | 0.76 | 25 | EDO |
| 4 | 111 | 0.41 | 0.76 | 21 | EDO |
| 5 | 84 | 0.39 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 462 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
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 Q8A1G2
- Elsewhere: RCSB PDB 3CK8 · PDBe 3CK8 · UniProt Q8A1G2
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