Research workbench
Designed armadillo-repeat protein
Analyse Designed armadillo-repeat protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DB8
- Type
- protein
- Length
- 970 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Armadillo-repeat protein
- Ligands
- MG
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Armadillo-repeat protein | protein | 247 | 73% helix, 0% strand | — |
| B | Armadillo-repeat protein | protein | 239 | 77% helix, 0% strand | — |
| C | Armadillo-repeat protein | protein | 238 | 79% helix, 0% strand | — |
| D | Armadillo-repeat protein | protein | 246 | 72% helix, 0% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 694 | 0.84 | 0.88 | 105 | empty |
| 2 | 984 | 0.80 | 0.82 | 139 | MG |
| 3 | 249 | 0.66 | 0.83 | 45 | MG |
| 4 | 148 | 0.54 | 0.81 | 21 | MG |
| 5 | 161 | 0.52 | 0.79 | 30 | empty |
Interfaces
6 interfaces between chains.
- A–D · 2336 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 2290 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 826 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 533 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 228 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4DB8 · Designed Armadillo-repeat 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 4DB8 · PDBe 4DB8
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