MolNFT v1 · #157163 · protein
Myotoxin II from bothrops moojeni complexed with rosmarinic acid
6MQD · Basic phospholipase A2 homolog 2: “Myotoxin II from bothrops moojeni complexed with rosmarinic acid”. X-ray diffraction, 1 ligand (ROA), 2 pockets (best druggability 0.67). MolNFT v1 #157163 on GenesisL1: 3D structure, binding sites…
- PDB
- 6MQD
- Type
- protein
- Length
- 244 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Basic phospholipase A2 homolog 2
- UniProt
- Q9I834
- Ligands
- ROA
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Basic phospholipase A2 homolog 2 | protein | 122 | 49% helix, 7% strand | Q9I834 |
Ligands and binding sites
- ROA · (2R)-3-(3,4-dihydroxyphenyl)-2-{[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}propanoic acid · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 266 | 0.67 | 0.83 | 37 | empty |
| 2 | 239 | 0.63 | 0.81 | 39 | empty |
Interfaces
1 interface between chains.
- A–B · 690 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 6MQD · Myotoxin II from Bothrops moojeni complexed with Rosmarinic Acid · the same entry in another collection · chain A against A, TM-score 1.00
- Q9I834 · AlphaFold monomer V2.0 prediction for basic phospholipase A2 homolog myotoxin II (Q9I834) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q9I834
- Elsewhere: RCSB PDB 6MQD · PDBe 6MQD · UniProt Q9I834
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