Research workbench
Agkistrodotoxin, a phospholipase A2-type presynaptic neurotoxin from agkistrodon halys pallas
Analyse Agkistrodotoxin, a phospholipase A2-type presynaptic neurotoxin from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1BJJ
- Type
- protein
- Length
- 732 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Agkistrodotoxin
- EC
- 3.1.1.4
- UniProt
- P14421
- Ligands
- CA
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Agkistrodotoxin (EC 3.1.1.4) | protein | 122 | 48% helix, 7% strand | P14421 |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains A, E, B, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 451 | 0.79 | 0.87 | 47 | empty |
| 2 | 317 | 0.73 | 0.85 | 41 | empty |
| 3 | 207 | 0.73 | 0.88 | 26 | empty |
| 4 | 409 | 0.73 | 0.83 | 43 | empty |
| 5 | 309 | 0.69 | 0.83 | 46 | empty |
Interfaces
9 interfaces between chains.
- B–C · 486 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 403 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 316 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 303 Ų buried · 5 hydrogen bonds · protein-protein
- C–F · 302 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 disulfide (disulfide).
Compared structures
- 1BJJ · Agkistrodotoxin, a phospholipase A2-type presynaptic neurotoxin from agkistrodon halys… · the same entry in another collection · chain C against C, TM-score 1.00
- P14421 · AlphaFold monomer V2.0 prediction for neutral phospholipase A2 agkistrodotoxin (P14421) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P14421
- Elsewhere: RCSB PDB 1BJJ · PDBe 1BJJ · UniProt P14421
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.