MolNFT v1 · #11292 · protein
Structure of a basic phospholipase A2 from agkistrodon halys pallas at 2.13A resolution
1JIA: “Structure of a basic phospholipase A2 from agkistrodon halys pallas at 2.13A resolution”. X-ray diffraction, 1 ligand (CA), 2 pockets (best druggability 0.73). MolNFT v1 #11292 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 1JIA
- Type
- protein
- Length
- 244 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase A2
- EC
- 3.1.1.4
- UniProt
- O42187
- Ligands
- CA
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phospholipase A2 (EC 3.1.1.4) | protein | 122 | 48% helix, 7% strand | O42187 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · 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 | 488 | 0.73 | 0.82 | 55 | empty |
| 2 | 130 | 0.56 | 0.83 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 367 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 1JIA · Structure of a basic phospholipase A2 from agkistrodon halys pallas at 2.13A resolution · 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 1JIA · PDBe 1JIA · UniProt O42187
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