Research workbench
AD5 knob in complex with a designed ankyrin repeat protein
Analyse AD5 knob in complex with a designed ankyrin repeat protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ATZ
- Type
- protein
- Length
- 989 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fiber protein; Designed ankyrin repeat protein
- UniProt
- P11818
- Pockets
- 10 · best druggability 0.68
Structure
x-ray diffraction · 5 distinct chains · 24% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fiber protein | protein | 182 | 9% helix, 40% strand | P11818 |
| B | Fiber protein | protein | 171 | 5% helix, 42% strand | P11818 |
| C | Fiber protein | protein | 176 | 6% helix, 41% strand | P11818 |
| D, E | Designed ankyrin repeat protein | protein | 154 | 55% helix, 0% strand | — |
| F | Designed ankyrin repeat protein | protein | 152 | 53% helix, 1% strand | — |
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 | 59 | 0.68 | 0.96 | 30 | empty |
| 2 | 457 | 0.61 | 0.75 | 57 | empty |
| 3 | 367 | 0.57 | 0.75 | 50 | empty |
| 4 | 326 | 0.53 | 0.74 | 49 | empty |
| 5 | 80 | 0.39 | 0.78 | 16 | empty |
Interfaces
7 interfaces between chains.
- A–B · 994 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 956 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 909 Ų buried · 12 hydrogen bonds · protein-protein
- C–F · 752 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 727 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4ATZ · Ad5 knob in complex with a designed ankyrin 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
- Every structure of UniProt P11818
- Elsewhere: RCSB PDB 4ATZ · PDBe 4ATZ · UniProt P11818
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