Research workbench
Crystal structure of prtx-I, a PLA2 homolog from bothrops pirajai
Analyse Crystal structure of prtx-I, a PLA2 homolog from bothrops pirajai in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Q2J
- Type
- protein
- Length
- 242 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase A2 homolog 1
- UniProt
- P58399
- Ligands
- SO4
- Pockets
- 1 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phospholipase A2 homolog 1 | protein | 121 | 50% helix, 7% strand | P58399 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 784 | 0.80 | 0.83 | 82 | empty |
Interfaces
1 interface between chains.
- A–B · 682 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 2Q2J · Crystal structure of PrTX-I, a PLA2 homolog from Bothrops pirajai · the same entry in another collection · chain A against A, TM-score 1.00
- P58399 · AlphaFold monomer V2.0 prediction for basic phospholipase A2 homolog piratoxin-1 (P58399) · 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 P58399
- Elsewhere: RCSB PDB 2Q2J · PDBe 2Q2J · UniProt P58399
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