Research workbench
Crystal structure of complex of phospholipase A2 with octyl sulfates
Analyse Crystal structure of complex of phospholipase A2 with octyl sulfates in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FVI
- Type
- protein
- Length
- 496 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase A2, major isoenzyme
- EC
- 3.1.1.4
- UniProt
- P00592
- Ligands
- OSF, CA, NA, CL
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Phospholipase A2, major isoenzyme (EC 3.1.1.4) | protein | 124 | 52% helix, 7% strand | P00592 |
Ligands and binding sites
- OSF · octyl sulfate · ligand · 12 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · chains C, D
- CL · Chloride ion · ion · 2 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 698 | 0.83 | 0.86 | 68 | OSF, NA |
| 2 | 500 | 0.79 | 0.86 | 61 | CL, OSF |
| 3 | 225 | 0.69 | 0.86 | 28 | empty |
| 4 | 220 | 0.66 | 0.84 | 32 | OSF |
| 5 | 81 | 0.54 | 0.86 | 28 | OSF |
Interfaces
6 interfaces between chains.
- C–D · 975 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 431 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 215 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 198 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 167 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 disulfide (disulfide).
Compared structures
- 3FVI · Crystal Structure of Complex of Phospholipase A2 with Octyl Sulfates · the same entry in another collection · chain A against A, TM-score 1.00
- P00592 · AlphaFold monomer V2.0 prediction for phospholipase A2, major isoenzyme (P00592) · 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 P00592
- Elsewhere: RCSB PDB 3FVI · PDBe 3FVI · UniProt P00592
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