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Crystal structure of lysophospholipase A2 conjugated with phenylmethylsulfonyl fluoride
Analyse Crystal structure of lysophospholipase A2 conjugated with phenylmethylsulfonyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BJE
- Type
- protein
- Length
- 437 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl-protein thioesterase 2
- EC
- 3.1.2.-
- UniProt
- O95372
- Ligands
- PMS
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acyl-protein thioesterase 2 (EC 3.1.2.-) | protein | 220 | 33% helix, 20% strand | O95372 |
| B | Acyl-protein thioesterase 2 (EC 3.1.2.-) | protein | 217 | 33% helix, 22% strand | O95372 |
Ligands and binding sites
- PMS · phenylmethanesulfonic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 242 | 0.77 | 0.90 | 35 | PMS |
| 2 | 119 | 0.45 | 0.78 | 22 | empty |
| 3 | 141 | 0.45 | 0.76 | 17 | empty |
| 4 | 159 | 0.42 | 0.74 | 30 | empty |
| 5 | 73 | 0.37 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 792 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6BJE · Crystal Structure of Lysophospholipase A2 Conjugated with Phenylmethylsulfonyl Fluoride · the same entry in another collection · chain A against A, TM-score 1.00
- O95372 · AlphaFold monomer V2.0 prediction for acyl-protein thioesterase 2 (O95372) · a predicted model of the same protein · chain B 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 O95372
- Elsewhere: RCSB PDB 6BJE · PDBe 6BJE · UniProt O95372
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