Research workbench
Crystal structure of mt-I isolated from bothrops asper venom.
Analyse Crystal structure of mt-I isolated from bothrops asper venom. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TFV
- Type
- protein
- Length
- 244 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Basic phospholipase A2 myotoxin III
- EC
- 3.1.1.4
- UniProt
- P20474
- Pockets
- 1 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Basic phospholipase A2 myotoxin III (EC 3.1.1.4) | protein | 122 | 45% helix, 8% strand | P20474 |
Ligands and binding sites
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 651 | 0.73 | 0.79 | 63 | empty |
Interfaces
1 interface between chains.
- A–B · 641 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 5TFV · Crystal Structure of MT-I isolated from Bothrops asper venom. · the same entry in another collection · chain A against A, TM-score 1.00
- P20474 · AlphaFold monomer V2.0 prediction for basic phospholipase A2 myotoxin I (P20474) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 P20474
- Elsewhere: RCSB PDB 5TFV · PDBe 5TFV · UniProt P20474
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