Research workbench
Design of specific inhibitors of phospholipase A2: crystal structure of a complex formed between phospholipase A2 from daboia russelli pulchella and a designed pentapeptide leu-ala-ile-tyr-ser at 2.0 resolution
Analyse Design of specific inhibitors of phospholipase A2: crystal structure of a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JQ8
- Type
- protein
- Length
- 247 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase A2; Peptide inhibitor
- EC
- 3.1.1.4
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phospholipase A2 (EC 3.1.1.4) | protein | 121 | 47% helix, 8% strand | — |
| P | Peptide inhibitor | 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
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 221 | 0.71 | 0.87 | 35 | empty |
| 2 | 152 | 0.59 | 0.83 | 23 | empty |
| 3 | 79 | 0.37 | 0.76 | 14 | empty |
| 4 | 85 | 0.35 | 0.75 | 17 | empty |
| 5 | 54 | 0.26 | 0.73 | 11 | empty |
Interfaces
3 interfaces between chains.
- A–B · 674 Ų buried · 2 hydrogen bonds · protein-protein
- A–P · 542 Ų buried · 7 hydrogen bonds · protein-protein
- B–P · 163 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 1JQ8 · Design of specific inhibitors of phospholipase A2: Crystal structure of a complex formed… · 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
- Elsewhere: RCSB PDB 1JQ8 · PDBe 1JQ8
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