Research workbench
Crystal structure of a ternary complex of phospholipase A2 with indomethacin and nimesulide at 2.9 a resolution
Analyse Crystal structure of a ternary complex of phospholipase A2 with indomethacin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OTH
- Type
- protein
- Length
- 121 residues
- Chains
- 1
- 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
- NIM, IMN, CCN
- Pockets
- 1 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospholipase A2 vrv-pl-viiia (EC 3.1.1.4) | protein | 121 | 49% helix, 8% strand | P59071 |
Ligands and binding sites
- NIM · 4-nitro-2-phenoxymethanesulfonanilide · ligand · chains A
- IMN · Indomethacin · ligand · chains A
- CCN · Acetonitrile · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 128 | 0.51 | 0.80 | 19 | empty |
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 2OTH · Crystal structure of a ternary complex of phospholipase A2 with indomethacin and… · the same entry in another collection · chain A against A, TM-score 1.00
- P59071 · AlphaFold monomer V2.0 prediction for basic phospholipase A2 vrv-pl- viiia (P59071) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 2OTH · PDBe 2OTH · UniProt P59071
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