Research workbench
2.05 a crystal structure of the amb a 11 cysteine protease, a major ragweed pollen allergen, in its proform
Analyse 2.05 a crystal structure of the amb a 11 cysteine protease, a major ragweed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EF4
- Type
- protein
- Length
- 650 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteine protease
- UniProt
- V5LU01
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cysteine protease | protein | 328 | 34% helix, 16% strand | V5LU01 |
| B | Cysteine protease | protein | 322 | 34% helix, 16% strand | V5LU01 |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 650 | 0.80 | 0.85 | 95 | empty |
| 2 | 123 | 0.50 | 0.80 | 24 | empty |
| 3 | 116 | 0.47 | 0.79 | 23 | GOL |
| 4 | 69 | 0.32 | 0.75 | 21 | empty |
| 5 | 58 | 0.26 | 0.72 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1542 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5EF4 · 2.05 A crystal structure of the Amb a 11 cysteine protease, a major ragweed pollen… · the same entry in another collection · chain A against A, TM-score 1.00
- V5LU01 · AlphaFold monomer V2.0 prediction for cysteine protease amb a 11.0101 (V5LU01) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 V5LU01
- Elsewhere: RCSB PDB 5EF4 · PDBe 5EF4 · UniProt V5LU01
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.