Research workbench
Crystal structure of a C49 Phospholipase A2 from Indian cobra reveals carbohydrate binding in the hydrophobic channel
Analyse Crystal structure of a C49 Phospholipase A2 from Indian cobra reveals… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OWS
- Type
- protein
- Length
- 236 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- Naja naja
- Molecule
- Phospholipase A2
- EC
- 3.1.1.4
- UniProt
- P15445
- Ligands
- NAG, ZN
- Pockets
- 1 · best druggability 0.81
Structure
x-ray diffraction · resolution 2.3 · 2 distinct chains · 49% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospholipase A2 (EC 3.1.1.4) | protein | 118 | 48% helix, 9% strand | P15445 |
| B | Phospholipase A2 (EC 3.1.1.4) | protein | 118 | 49% helix, 9% strand | P15445 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- ZN · Zinc ion · metal · 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 | 1006 | 0.81 | 0.82 | 68 | NAG |
Interfaces
1 interface between chains.
- A–B · 666 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide (disulfide).
Compared structures
- 1OWS · Crystal structure of a C49 phospholipase A2 from indian cobra reveals carbohydrate… · the same entry in another collection · chain A against A, TM-score 1.00
- P15445 · AlphaFold monomer V2.0 prediction for acidic phospholipase A2 2 (P15445) · 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 P15445
- Elsewhere: RCSB PDB 1OWS · PDBe 1OWS · UniProt P15445
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