MolNFT v1 · #52958 · protein
Structure of oryza sativa (rice) PLA2, complex with octanoic acid
2WG9 · Putative phospholipase A2: “Structure of oryza sativa (rice) PLA2, complex with octanoic acid”. X-ray diffraction, 3 ligands (OCA, CA, NA), 2 pockets (best druggability 0.65). MolNFT v1 #52958 on GenesisL1: 3D structure, binding…
- PDB
- 2WG9
- Type
- protein
- Length
- 228 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative phospholipase A2
- EC
- 3.1.1.4
- UniProt
- Q9XG81
- Ligands
- OCA, CA, NA
- Pockets
- 2 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative phospholipase A2 (EC 3.1.1.4) | protein | 114 | 44% helix, 8% strand | Q9XG81 |
Ligands and binding sites
- OCA · Octanoic acid (caprylic acid) · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 342 | 0.65 | 0.80 | 47 | OCA |
| 2 | 306 | 0.62 | 0.79 | 33 | OCA |
Interfaces
1 interface between chains.
- A–B · 1067 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 2WG9 · Structure of Oryza Sativa (Rice) PLA2, complex with octanoic acid · 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 2WG9 · PDBe 2WG9 · UniProt Q9XG81
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