MolNFT v1 · #71688 · protein
Crystal structure of bn IV in complex with myristic acid: a LYS49 myotoxic phospholipase A2 from bothrops neuwiedi venom
3MLM · Bn-IV lys-49 phospholipase A2: “Crystal structure of bn IV in complex with myristic acid: a LYS49 myotoxic phospholipase A2 from bothrops…”. X-ray diffraction, 2 ligands (MYR, SO4), 4 pockets (best druggability 0.50). MolNFT v1…
- PDB
- 3MLM
- Type
- protein
- Length
- 242 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bn-IV lys-49 phospholipase A2
- EC
- 3.1.1.4
- UniProt
- Q9IAT9
- Ligands
- MYR, SO4
- Pockets
- 4 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bn-IV lys-49 phospholipase A2 (EC 3.1.1.4) | protein | 121 | 46% helix, 7% strand | Q9IAT9 |
Ligands and binding sites
- MYR · Myristic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 134 | 0.50 | 0.79 | 23 | MYR |
| 2 | 122 | 0.49 | 0.79 | 20 | MYR |
| 3 | 62 | 0.39 | 0.80 | 21 | empty |
| 4 | 56 | 0.32 | 0.76 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 424 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 3MLM · Crystal structure of Bn IV in complex with myristic acid: A Lys49 myotoxic phospholipase… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9IAT9 · AlphaFold monomer V2.0 prediction for basic phospholipase A2 homolog bnsp-7 (Q9IAT9) · 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 Q9IAT9
- Elsewhere: RCSB PDB 3MLM · PDBe 3MLM · UniProt Q9IAT9
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