Research workbench
Designed armadillo repeat protein (YIIM3AII)
Analyse Designed armadillo repeat protein (YIIM3AII) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DBA
- Type
- protein
- Length
- 784 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Designed armadillo repeat protein, YIIM3AII
- Pockets
- 10 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Designed armadillo repeat protein, YIIM3AII | protein | 196 | 77% helix, 0% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 5 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 463 | 0.67 | 0.79 | 70 | empty |
| 2 | 701 | 0.67 | 0.75 | 40 | GOL |
| 3 | 450 | 0.65 | 0.78 | 76 | empty |
| 4 | 480 | 0.64 | 0.77 | 53 | empty |
| 5 | 153 | 0.39 | 0.73 | 25 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2105 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 2041 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 250 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 191 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 186 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4DBA · Designed Armadillo repeat protein (YIIM3AII) · 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 4DBA · PDBe 4DBA
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