Research workbench
Crystal structure of a complex formed between phospholipase A2 from daboia russelli pulchella and a designed pentapeptide phe-leu-ser- tyr-lys at 1.8 resolution
Analyse Crystal structure of a complex formed between phospholipase A2 from daboia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JQ9
- 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
- UniProt
- P59071
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phospholipase A2 (EC 3.1.1.4) | protein | 121 | 47% helix, 7% strand | P59071 |
| P | Peptide inhibitor | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACY · Acetic acid · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 342 | 0.73 | 0.85 | 47 | empty |
| 2 | 227 | 0.59 | 0.80 | 31 | empty |
| 3 | 72 | 0.30 | 0.73 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 685 Ų buried · 1 hydrogen bond · protein-protein
- A–P · 575 Ų buried · 11 hydrogen bonds · protein-protein
- B–P · 202 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 1JQ9 · Crystal structure of a complex formed between phospholipase A2 from Daboia russelli… · 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 1JQ9 · PDBe 1JQ9 · UniProt P59071
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