Research workbench

Carboxylic ester hydrolase, P 1 21 1 space group

Analyse Carboxylic ester hydrolase, P 1 21 1 space group in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1LE6
Type: protein
Length: 369 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Group X secretory phospholipase A2
EC: 3.1.1.4
UniProt: O15496
Ligands: CA
Pockets: 6 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Group X secretory phospholipase A2 (EC 3.1.1.4)	protein	123	46% helix, 9% strand	O15496

Ligands and binding sites

CA · Calcium ion · metal · 3 copies · chains A, B, C
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains B, A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	260	0.63	0.81	26	empty
2	242	0.59	0.79	27	MPD
3	275	0.58	0.78	23	empty
4	306	0.56	0.75	24	empty
5	95	0.33	0.73	21	empty

Interfaces

3 interfaces between chains.

B–C · 367 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 347 Å² buried · 1 hydrogen bond · protein-protein
A–C · 40 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 disulfide (disulfide).

Compared structures

1LE6 · Carboxylic ester hydrolase, P 1 21 1 space group · the same entry in another collection · chain A against A, TM-score 1.00
O15496 · AlphaFold monomer V2.0 prediction for group 10 secretory phospholipase A2 (O15496) · 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 O15496
Elsewhere: RCSB PDB 1LE6 · PDBe 1LE6 · UniProt O15496

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.