Research workbench
Crystal structure of the platelet activator convulxin, a disulfide linked A4B4 cyclic tetramer from the venom of crotalus durissus terrificus
Analyse Crystal structure of the platelet activator convulxin, a disulfide linked A4B4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1UMR
- Type
- protein
- Length
- 520 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Convulxin alpha; Convulxin beta
- UniProt
- O93426, O93427
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Convulxin alpha | protein | 135 | 23% helix, 30% strand | O93426 |
| C, D | Convulxin beta | protein | 125 | 18% helix, 33% strand | O93427 |
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 447 | 0.62 | 0.76 | 52 | empty |
| 2 | 378 | 0.60 | 0.76 | 38 | empty |
| 3 | 193 | 0.47 | 0.75 | 31 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1926 Ų buried · 32 hydrogen bonds · protein-protein
- B–D · 1910 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 326 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 233 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 61 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 1UMR · Crystal structure of the platelet activator convulxin, a disulfide linked a4b4 cyclic… · the same entry in another collection · chain A against A, TM-score 1.00
- O93427 · AlphaFold monomer V2.0 prediction for snaclec convulxin subunit beta (O93427) · a predicted model of the same protein · chain C against A, TM-score 0.99
- O93426 · AlphaFold monomer V2.0 prediction for snaclec convulxin subunit alpha (O93426) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O93426
- Every structure of UniProt O93427
- Elsewhere: RCSB PDB 1UMR · PDBe 1UMR · UniProt O93426 · UniProt O93427
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