Research workbench
LYS49 PLA2 bpii derived from the venom of protobothrops flavoviridis.
Analyse LYS49 PLA2 bpii derived from the venom of protobothrops flavoviridis. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AL3
- Type
- protein
- Length
- 488 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Basic phospholipase A2 bp-II
- EC
- 3.1.1.4
- UniProt
- P0DJJ9
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Basic phospholipase A2 bp-II (EC 3.1.1.4) | protein | 122 | 45% helix, 5% strand | P0DJJ9 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 545 | 0.74 | 0.82 | 69 | empty |
| 2 | 134 | 0.58 | 0.83 | 21 | empty |
| 3 | 145 | 0.54 | 0.81 | 26 | empty |
| 4 | 54 | 0.37 | 0.79 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–C · 693 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 462 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 423 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 39 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 37 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide (disulfide).
Compared structures
- 6AL3 · Lys49 PLA2 BPII derived from the venom of Protobothrops flavoviridis. · the same entry in another collection · chain A against A, TM-score 1.00
- P0DJJ9 · AlphaFold monomer V2.0 prediction for basic phospholipase A2 bp-II (P0DJJ9) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P0DJJ9
- Elsewhere: RCSB PDB 6AL3 · PDBe 6AL3 · UniProt P0DJJ9
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