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MolNFT v1 · #25275 · protein

A re-determination of the structure of the triple mutant (K53,56,120M) of phospholipase A2 at 1.6A resolution using sulphur-sas at 1.54A wavelength

1VKQ: “A re-determination of the structure of the triple mutant (K53,56,120M) of phospholipase A2 at 1.6A resolution…”. X-ray diffraction, 2 ligands (CA, CL), 1 pocket (best druggability 0.59). MolNFT v1 #25275 on GenesisL1: 3D structure…

PDB
1VKQ
Type
protein
Length
123 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Phospholipase A2
EC
3.1.1.4
UniProt
P00593
Ligands
CA, CL
Pockets
1 · best druggability 0.59

Structure

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

ChainMoleculeTypeResiduesSecondary structureUniProt
APhospholipase A2 (EC 3.1.1.4)protein12346% helix, 9% strandP00593

Ligands and binding sites

  • CA · Calcium ion · metal · chains A
  • CL · Chloride ion · ion · chains A
  • MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · 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.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11350.590.8423MPD

Modifications

Observed in the structure: 7 disulfide (disulfide).

Compared structures

  • 1VKQ · A re-determination of the structure of the triple mutant (K53,56,120M) of phospholipase… · the same entry in another collection · chain A against A, TM-score 1.00
  • P00593 · AlphaFold monomer V2.0 prediction for phospholipase A2 (P00593) · a predicted model of the same protein · chain A against A, TM-score 0.97

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