Research workbench
Structure of daboiatoxin (heterodimeric PLA2 venom)
Analyse Structure of daboiatoxin (heterodimeric PLA2 venom) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2H4C
- Type
- protein
- Length
- 976 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase A2-III; Phospholipase A2-II
- EC
- 3.1.1.4
- UniProt
- Q7T2R1, Q7T3T5
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Phospholipase A2-III (EC 3.1.1.4) | protein | 122 | 34% helix, 5% strand | Q7T2R1 |
| B, D, F, H | Phospholipase A2-II (EC 3.1.1.4) | protein | 122 | 38% helix, 9% strand | Q7T3T5 |
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 370 | 0.82 | 0.90 | 50 | empty |
| 2 | 403 | 0.82 | 0.90 | 53 | empty |
| 3 | 332 | 0.79 | 0.89 | 50 | empty |
| 4 | 264 | 0.78 | 0.90 | 46 | empty |
| 5 | 185 | 0.60 | 0.82 | 32 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1406 Ų buried · 16 hydrogen bonds · protein-protein
- G–H · 1401 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 1343 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1293 Ų buried · 10 hydrogen bonds · protein-protein
- B–G · 139 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide (disulfide).
Compared structures
- 2H4C · Structure of Daboiatoxin (heterodimeric PLA2 venom) · the same entry in another collection · chain H against H, TM-score 1.00
- Q7T3T5 · AlphaFold monomer V2.0 prediction for acidic phospholipase A2 daboiatoxin B chain (Q7T3T5) · a predicted model of the same protein · chain B against A, TM-score 0.93
- Q7T2R1 · AlphaFold monomer V2.0 prediction for acidic phospholipase A2 daboiatoxin a chain (Q7T2R1) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 Q7T2R1
- Every structure of UniProt Q7T3T5
- Elsewhere: RCSB PDB 2H4C · PDBe 2H4C · UniProt Q7T2R1 · UniProt Q7T3T5
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