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MolNFT v1 · #29076 · protein

Crystal structure of a novel phospholipase A2 from naja naja sagittifera with a strong anticoagulant activity

1YXH: “Crystal structure of a novel phospholipase A2 from naja naja sagittifera with a strong anticoagulant activity”. X-ray diffraction, 2 ligands (CA, PO4), 1 pocket (best druggability 0.51). MolNFT v1 #29076 on GenesisL1: 3D structure…

PDB
1YXH
Type
protein
Length
119 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Phospholipase A2
EC
3.1.1.4
UniProt
Q6T179
Ligands
CA, PO4
Pockets
1 · best druggability 0.51

Structure

x-ray diffraction · 1 distinct chain · 48% helix, 11% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
APhospholipase A2 (EC 3.1.1.4)protein11948% helix, 11% strandQ6T179

Ligands and binding sites

  • CA · Calcium ion · metal · chains A
  • PO4 · Phosphate ion · ion · chains A
  • EOH · Ethanol · additive · 2 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
11210.510.8018EOH

Modifications

Observed in the structure: 7 disulfide (disulfide).

Compared structures

  • 1YXH · Crystal structure of a novel phospholipase A2 from Naja naja sagittifera with a strong… · the same entry in another collection · chain A against A, TM-score 1.00
  • Q6T179 · AlphaFold monomer V2.0 prediction for acidic phospholipase A2 4 (Q6T179) · a predicted model of the same protein · chain A against A, TM-score 0.99

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