Research workbench
Non-specific binding to phospholipase A2:CRYSTAL structure of the complex of PLA2 with a designed peptide tyr-TRP-ala- ala-ala-ala at 1.7A resolution
Analyse Non-specific binding to phospholipase A2:CRYSTAL structure of the complex of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TDV
- Type
- protein
- Length
- 127 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase A2 vrv-pl-viiia; Ywaaaa
- EC
- 3.1.1.4
- UniProt
- P59071
- Ligands
- SO4
- Pockets
- 1 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospholipase A2 vrv-pl-viiia (EC 3.1.1.4) | protein | 121 | 48% helix, 8% strand | P59071 |
| B | Ywaaaa | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · 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 | 162 | 0.50 | 0.78 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 234 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 1TDV · Non-specific binding to phospholipase A2:Crystal structure of the complex of PLA2 with a… · 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 1TDV · PDBe 1TDV · UniProt P59071
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.