Research workbench
Design of specific inhibitors of phospholipase A2: crystal structure of the complex formed between a group II cys 49 phospholipase A2 and a designed pentapeptide ala-leu-ala- ser-lys at 2.6A resolution
Analyse Design of specific inhibitors of phospholipase A2: crystal structure of the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DO2
- Type
- protein
- Length
- 126 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase A2 vrv-pl-viiia; Ala-leu-ala-ser-lys
- EC
- 3.1.1.4
- UniProt
- P59071
- Ligands
- SO4
- Pockets
- 1 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospholipase A2 vrv-pl-viiia (EC 3.1.1.4) | protein | 121 | 48% helix, 9% strand | P59071 |
| P | Ala-leu-ala-ser-lys | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 115 | 0.63 | 0.87 | 23 | empty |
Interfaces
1 interface between chains.
- A–P · 366 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 2DO2 · Design of specific inhibitors of phospholipase A2: Crystal structure of the complex… · 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 0.98
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 P59071
- Elsewhere: RCSB PDB 2DO2 · PDBe 2DO2 · UniProt P59071
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