Research workbench
Crystal structure of the complex of type II phospholipase A2 with a designed peptide inhibitor phe - leu - ala - tyr - lys at 1.69 a resolution
Analyse Crystal structure of the complex of type II phospholipase A2 with a designed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GLD
- 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; Flayk
- EC
- 3.1.1.4
- UniProt
- D0VX11
- Ligands
- SO4
- Pockets
- 1 · best druggability 0.26
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 | D0VX11 |
| B | Flayk | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
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 | 54 | 0.26 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 542 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 4GLD · Crystal Structure of the complex of type II phospholipase A2 with a designed peptide… · the same entry in another collection · chain A against A, TM-score 1.00
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 D0VX11
- Elsewhere: RCSB PDB 4GLD · PDBe 4GLD · UniProt D0VX11
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