Research workbench
Designed ankyrin repeat protein (darpin) vhah-1 in complex with lysozyme
Analyse Designed ankyrin repeat protein (darpin) vhah-1 in complex with lysozyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OOY
- Type
- protein
- Length
- 575 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Darpin vhah-1; Lysozyme C
- EC
- 3.2.1.17
- UniProt
- P00698
- Pockets
- 2 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Darpin vhah-1 | protein | 161 | 56% helix, 0% strand | — |
| B, F | Lysozyme C (EC 3.2.1.17) | protein | 129 | 42% helix, 11% strand | P00698 |
| E | Darpin vhah-1 | protein | 156 | 54% helix, 0% strand | — |
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 396 | 0.64 | 0.78 | 46 | empty |
| 2 | 384 | 0.64 | 0.79 | 45 | empty |
Interfaces
5 interfaces between chains.
- E–F · 933 Ų buried · 11 hydrogen bonds · protein-protein
- B–F · 932 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 895 Ų buried · 10 hydrogen bonds · protein-protein
- A–F · 57 Ų buried · 2 hydrogen bonds · protein-protein
- B–E · 55 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5OOY · Designed Ankyrin Repeat Protein (DARPin) VHAH-1 in complex with Lysozyme · 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 P00698
- Elsewhere: RCSB PDB 5OOY · PDBe 5OOY · UniProt P00698
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