Research workbench
The atomic resolution crystal structure of the phospholipase A2 (PLA2) complex with nimesulide reveals its weaker binding to PLA2
Analyse The atomic resolution crystal structure of the phospholipase A2 (PLA2) complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZWP
- Type
- protein
- Length
- 121 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase A2 vrv-pl-viiia
- EC
- 3.1.1.4
- UniProt
- P59071
- Ligands
- NIM, SO4
- Pockets
- 1 · best druggability 0.45
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospholipase A2 vrv-pl-viiia (EC 3.1.1.4) | protein | 121 | 48% helix, 7% strand | P59071 |
Ligands and binding sites
- NIM · 4-nitro-2-phenoxymethanesulfonanilide · ligand · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A
- MOH · Methanol · 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 | 106 | 0.45 | 0.79 | 21 | empty |
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 1ZWP · The atomic resolution Crystal structure of the Phospholipase A2 (PLA2) complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P59071 · AlphaFold monomer V2.0 prediction for basic phospholipase A2 vrv-pl- viiia (P59071) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P59071
- Elsewhere: RCSB PDB 1ZWP · PDBe 1ZWP · UniProt P59071
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