MolNFT v1 · #181556 · protein
Myotoxin I from bothrops moojeni co-crystallized with synthetic inhibitor varespladib (LY315920)
7LYE · Basic phospholipase A2 homolog bomotx: “Myotoxin I from bothrops moojeni co-crystallized with synthetic inhibitor varespladib (LY315920)”. X-ray diffraction, 1 ligand (VRD), 5 pockets (best druggability 0.56). MolNFT v1 #181556 on…
- PDB
- 7LYE
- Type
- protein
- Length
- 488 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Basic phospholipase A2 homolog bomotx
- UniProt
- A0A1S5XW05
- Ligands
- VRD
- Pockets
- 5 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Basic phospholipase A2 homolog bomotx | protein | 122 | 46% helix, 7% strand | A0A1S5XW05 |
Ligands and binding sites
- VRD · ({3-[amino(oxo)acetyl]-1-benzyl-2-ethyl-1H-indol-4-yl}oxy)acetic acid · ligand · 4 copies · chains A, B, C, D
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 174 | 0.56 | 0.80 | 22 | VRD |
| 2 | 175 | 0.55 | 0.80 | 24 | VRD |
| 3 | 182 | 0.54 | 0.78 | 25 | VRD |
| 4 | 154 | 0.52 | 0.79 | 23 | VRD |
| 5 | 117 | 0.40 | 0.75 | 22 | PE4 |
Interfaces
4 interfaces between chains.
- C–D · 407 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 399 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 198 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 138 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 28 disulfide (disulfide).
Compared structures
- 7LYE · Myotoxin I from Bothrops moojeni co-crystallized with synthetic inhibitor Varespladib… · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A1S5XW05
- Elsewhere: RCSB PDB 7LYE · PDBe 7LYE · UniProt A0A1S5XW05
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