Research workbench
Crystal structure of the computationally designed CAKE6 protein
Analyse Crystal structure of the computationally designed CAKE6 protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TJF
- Type
- protein
- Length
- 1,440 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CAKE6
- Pockets
- 14 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | CAKE6 | protein | 240 | 0% helix, 43% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 7 copies · chains A, E, B, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 654 | 0.77 | 0.83 | 82 | empty |
| 2 | 115 | 0.74 | 0.95 | 33 | empty |
| 3 | 385 | 0.72 | 0.84 | 60 | GOL |
| 4 | 57 | 0.71 | 0.98 | 19 | empty |
| 5 | 495 | 0.65 | 0.77 | 32 | empty |
Interfaces
11 interfaces between chains.
- A–E · 2247 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 2163 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1810 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 1692 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 715 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6TJF · Crystal structure of the computationally designed Cake6 protein · 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
- Elsewhere: RCSB PDB 6TJF · PDBe 6TJF
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