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Crystal structure of a carbohydrate induced dimer of group I phospholipase A2 from bungarus caeruleus at 2.1 a resolution
Analyse Crystal structure of a carbohydrate induced dimer of group I phospholipase A2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1U4J
- Type
- protein
- Length
- 236 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase A2 isoform 2
- EC
- 3.1.1.4
- UniProt
- Q6SLM1
- Ligands
- MAN, NA, CL
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phospholipase A2 isoform 2 (EC 3.1.1.4) | protein | 118 | 45% helix, 8% strand | Q6SLM1 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- ACY · Acetic acid · additive · 3 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 560 | 0.80 | 0.85 | 49 | MAN |
| 2 | 99 | 0.57 | 0.86 | 29 | empty |
| 3 | 110 | 0.55 | 0.84 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 858 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 1U4J · Crystal structure of a carbohydrate induced dimer of group I phospholipase A2 from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6SLM1 · AlphaFold monomer V2.0 prediction for basic phospholipase A2 2 (Q6SLM1) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q6SLM1
- Elsewhere: RCSB PDB 1U4J · PDBe 1U4J · UniProt Q6SLM1
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