Research workbench
Crystal structure of AhV_bPA, a basic PLA2 from Agkistrodon halys pallas venom
Analyse Crystal structure of AhV_bPA, a basic PLA2 from Agkistrodon halys pallas venom in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HG9
- Type
- protein
- Length
- 488 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.6
- Source
- Gloydius halys
- Molecule
- Basic phospholipase A2 B
- EC
- 3.1.1.4
- UniProt
- O42187
- Ligands
- G3P, CA
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · resolution 1.6 · 1 distinct chain · 48% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Basic phospholipase A2 B (EC 3.1.1.4) | protein | 122 | 48% helix, 7% strand | O42187 |
Ligands and binding sites
- G3P · Sn-glycerol-3-phosphate · ligand · 2 copies · chains A, C
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains B, C
- CIT · Citric acid · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 255 | 0.81 | 0.93 | 47 | empty |
| 2 | 229 | 0.80 | 0.93 | 39 | GOL |
| 3 | 184 | 0.77 | 0.93 | 37 | G3P |
| 4 | 159 | 0.74 | 0.92 | 35 | G3P |
| 5 | 78 | 0.35 | 0.76 | 15 | CIT |
Interfaces
6 interfaces between chains.
- A–D · 668 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 605 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 453 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 338 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 312 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 28 disulfide (disulfide).
Compared structures
- 4HG9 · Crystal structure of AHV_BPA, a basic PLA2 from agkistrodon halys pallas venom · the same entry in another collection · chain A against A, TM-score 1.00
- O42187 · AlphaFold monomer V2.0 prediction for basic phospholipase A2 B (O42187) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O42187
- Elsewhere: RCSB PDB 4HG9 · PDBe 4HG9 · UniProt O42187
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