Research workbench
B. thetaiotaomicron susd with alpha-cyclodextrin
Analyse B. thetaiotaomicron susd with alpha-cyclodextrin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CK7
- Type
- protein
- Length
- 1,988 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Susd
- UniProt
- Q8A1G2
- Ligands
- GLC, CA
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Susd | protein | 496 | 45% helix, 6% strand | Q8A1G2 |
| B, C | Susd | protein | 497 | 45% helix, 6% strand | Q8A1G2 |
| D | Susd | protein | 498 | 45% helix, 6% strand | Q8A1G2 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 12 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 517 | 0.74 | 0.82 | 79 | empty |
| 2 | 297 | 0.67 | 0.82 | 46 | empty |
| 3 | 295 | 0.67 | 0.82 | 35 | GLC |
| 4 | 266 | 0.66 | 0.82 | 31 | GLC |
| 5 | 191 | 0.62 | 0.83 | 28 | empty |
Interfaces
6 interfaces between chains.
- A–D · 387 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 365 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 311 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 303 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 208 Ų buried · 5 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 3CK7 · PDBe 3CK7 · UniProt Q8A1G2
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