Research workbench
Crystal structure of the snake venom toxin aggretin
Analyse Crystal structure of the snake venom toxin aggretin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BX4
- Type
- protein
- Length
- 511 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aggretin alpha chain; Aggretin beta chain
- UniProt
- Q9I841, Q9I840
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 19% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aggretin alpha chain | protein | 132 | 20% helix, 31% strand | Q9I841 |
| B | Aggretin beta chain | protein | 122 | 17% helix, 34% strand | Q9I840 |
| C | Aggretin alpha chain | protein | 134 | 20% helix, 31% strand | Q9I841 |
| D | Aggretin beta chain | protein | 123 | 20% helix, 39% strand | Q9I840 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 552 | 0.77 | 0.84 | 56 | SO4 |
| 2 | 125 | 0.46 | 0.78 | 21 | GOL |
| 3 | 108 | 0.45 | 0.79 | 20 | SO4 |
| 4 | 62 | 0.30 | 0.75 | 20 | empty |
| 5 | 58 | 0.29 | 0.75 | 14 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1949 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1935 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 976 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 174 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 154 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 3BX4 · Crystal structure of the snake venom toxin aggretin · the same entry in another collection · chain B against B, TM-score 1.00
- Q9I841 · AlphaFold monomer V2.0 prediction for snaclec rhodocytin subunit alpha (Q9I841) · a predicted model of the same protein · chain A against A, TM-score 0.96
- Q9I840 · AlphaFold monomer V2.0 prediction for snaclec rhodocytin subunit beta (Q9I840) · a predicted model of the same protein · chain D against A, TM-score 0.95
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 Q9I841
- Every structure of UniProt Q9I840
- Elsewhere: RCSB PDB 3BX4 · PDBe 3BX4 · UniProt Q9I841 · UniProt Q9I840
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