Research workbench
Structure of oryza sativa (rice) PLA2, orthorhombic crystal form
Analyse Structure of oryza sativa (rice) PLA2, orthorhombic crystal form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WG8
- Type
- protein
- Length
- 331 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative phospholipase A2
- EC
- 3.1.1.4
- UniProt
- Q9XG81
- Ligands
- CA, NA
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative phospholipase A2 (EC 3.1.1.4) | protein | 108 | 44% helix, 8% strand | Q9XG81 |
| B | Putative phospholipase A2 (EC 3.1.1.4) | protein | 116 | 44% helix, 8% strand | Q9XG81 |
| C | Putative phospholipase A2 (EC 3.1.1.4) | protein | 107 | 44% helix, 8% strand | Q9XG81 |
Ligands and binding sites
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 | 887 | 0.81 | 0.83 | 88 | empty |
| 2 | 186 | 0.61 | 0.82 | 25 | empty |
| 3 | 87 | 0.47 | 0.81 | 26 | empty |
Interfaces
2 interfaces between chains.
- A–B · 939 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 523 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 2WG8 · Structure of Oryza Sativa (Rice) PLA2, orthorhombic crystal form · the same entry in another collection · chain A against A, TM-score 1.00
- Q9XG81 · AlphaFold monomer V2.0 prediction for probable phospholipase A2 homolog 2 (Q9XG81) · 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 Q9XG81
- Elsewhere: RCSB PDB 2WG8 · PDBe 2WG8 · UniProt Q9XG81
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