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Crystal structure of the ternary complex of phospholipase A2 with ajmaline and anisic acid at 3.1 a resolution
Analyse Crystal structure of the ternary complex of phospholipase A2 with ajmaline and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CBI
- Type
- protein
- Length
- 484 residues
- Chains
- 4
- 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
- AJM, ANN
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Phospholipase A2 vrv-pl-viiia (EC 3.1.1.4) | protein | 121 | 40% helix, 3% strand | P59071 |
Ligands and binding sites
- AJM · Ajmaline · ligand · 4 copies · chains C, B, A, D
- ANN · 4-methoxybenzoic acid · ligand · 4 copies · chains C, B, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 793 | 0.76 | 0.80 | 59 | empty |
| 2 | 777 | 0.75 | 0.79 | 58 | empty |
| 3 | 274 | 0.64 | 0.81 | 34 | ANN |
| 4 | 154 | 0.55 | 0.81 | 21 | ANN |
| 5 | 159 | 0.54 | 0.80 | 19 | ANN |
Interfaces
3 interfaces between chains.
- A–B · 618 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 554 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 399 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide (disulfide).
Compared structures
- 3CBI · Crystal structure of the ternary complex of phospholipase A2 with ajmaline and anisic… · 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
- Every structure of UniProt P59071
- Elsewhere: RCSB PDB 3CBI · PDBe 3CBI · UniProt P59071
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