Research workbench
Crystal structure of a novel phospholipase A2 from naja naja sagittifera at 1.5 a resolution
Analyse Crystal structure of a novel phospholipase A2 from naja naja sagittifera at 1.5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YXL
- Type
- protein
- Length
- 119 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase A2 isoform 3
- EC
- 3.1.1.4
- UniProt
- P60045
- Ligands
- CA, PO4
- Pockets
- 1 · best druggability 0.48
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospholipase A2 isoform 3 (EC 3.1.1.4) | protein | 119 | 48% helix, 11% strand | P60045 |
Ligands and binding sites
- CA · Calcium ion · metal · chains A
- PO4 · Phosphate ion · ion · chains A
- ACY · Acetic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 88 | 0.48 | 0.81 | 17 | ACY |
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 1YXL · Crystal structure of a novel phospholipase A2 from Naja naja sagittifera at 1.5 A… · the same entry in another collection · chain A against A, TM-score 1.00
- P60045 · AlphaFold monomer V2.0 prediction for acidic phospholipase A2 3 (P60045) · 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 P60045
- Elsewhere: RCSB PDB 1YXL · PDBe 1YXL · UniProt P60045
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