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MolNFT v1 · #13517 · protein

Carboxylic ester hydrolase, C 2 2 21 space group

1LE7 · Group X secretory phospholipase A2: “Carboxylic ester hydrolase, C 2 2 21 space group”. X-ray diffraction, 1 ligand (CA), 3 pockets (best druggability 0.62). MolNFT v1 #13517 on GenesisL1: 3D structure, binding sites and pockets in…

PDB
1LE7
Type
protein
Length
246 residues
Chains
2
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
3 · best druggability 0.62

Structure

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

ChainMoleculeTypeResiduesSecondary structureUniProt
A, BGroup X secretory phospholipase A2 (EC 3.1.1.4)protein12346% helix, 9% strandO15496

Ligands and binding sites

  • CA · Calcium ion · metal · 2 copies · chains A, B
  • MPD · (4S)-2-methyl-2,4-pentanediol · additive · 5 copies · chains A, B

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.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
12540.620.8027CA, MPD
22100.560.7922MPD
3890.420.7922empty

Interfaces

1 interface between chains.

  • A–B · 447 Ų buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

  • 1LE7 · CARBOXYLIC ESTER HYDROLASE, C 2 2 21 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 0.99

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