Research workbench
8-bladed beta-propeller formed by two 4-bladed fragments
Analyse 8-bladed beta-propeller formed by two 4-bladed fragments in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6R5Y
- Type
- protein
- Length
- 978 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wd-40 repeat protein
- UniProt
- B2J0I0
- Ligands
- ZN
- Pockets
- 14 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 1% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Wd-40 repeat protein | protein | 167 | 2% helix, 53% strand | B2J0I0 |
| B, C | Wd-40 repeat protein | protein | 162 | 0% helix, 54% strand | B2J0I0 |
| D, E | Wd-40 repeat protein | protein | 160 | 0% helix, 54% strand | B2J0I0 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1099 | 0.89 | 0.91 | 94 | empty |
| 2 | 1180 | 0.84 | 0.84 | 70 | empty |
| 3 | 869 | 0.76 | 0.80 | 82 | empty |
| 4 | 406 | 0.66 | 0.79 | 36 | empty |
| 5 | 340 | 0.65 | 0.80 | 37 | empty |
Interfaces
11 interfaces between chains.
- A–B · 1530 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 1427 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1427 Ų buried · 10 hydrogen bonds · protein-protein
- C–E · 347 Ų buried · 6 hydrogen bonds · protein-protein
- B–F · 340 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6R5Y · 8-bladed beta-propeller formed by two 4-bladed fragments · 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 B2J0I0
- Elsewhere: RCSB PDB 6R5Y · PDBe 6R5Y · UniProt B2J0I0
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