Research workbench
Crystal structure of the complex of group II PHOSPHOLIPASEA2 dimer with a fatty acid tridecanoic acid at 2.4 a resolution
Analyse Crystal structure of the complex of group II PHOSPHOLIPASEA2 dimer with a fatty… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TP2
- Type
- protein
- Length
- 242 residues
- Chains
- 2
- 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
- TDA, SO4
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phospholipase A2 vrv-pl-viiia (EC 3.1.1.4) | protein | 121 | 48% helix, 7% strand | P59071 |
Ligands and binding sites
- TDA · N-tridecanoic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A, B
- ACY · Acetic acid · additive · chains A
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 | 498 | 0.77 | 0.84 | 64 | TDA |
| 2 | 156 | 0.54 | 0.80 | 21 | TDA |
| 3 | 50 | 0.27 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 573 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 1TP2 · Crystal structure of the complex of group II phospholipaseA2 dimer with a fatty acid… · 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 1TP2 · PDBe 1TP2 · UniProt P59071
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