GL1X · GenesisL1 explorer

MolNFT v1 · #106640 · protein

Structure of protease

4TKX · Lys-gingipain W83: “Structure of protease”. X-ray diffraction, 5 ligands (TCK, NA, K), 1 pocket (best druggability 0.64). MolNFT v1 #106640 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
4TKX
Type
protein
Length
452 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Lys-gingipain W83
EC
3.4.22.47
UniProt
Q51817
Ligands
TCK, NA, K, PB, SO4
Pockets
1 · best druggability 0.64

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 25% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
LLys-gingipain W83 (EC 3.4.22.47)protein45230% helix, 25% strandQ51817

Ligands and binding sites

  • TCK · N-[(1S)-5-amino-1-(chloroacetyl)pentyl]-4-methylbenzenesulfonamide · ligand · chains L
  • NA · Sodium ion · metal · 2 copies · chains L
  • K · Potassium ion · metal · chains L
  • PB · Lead (II) ion · metal · chains L
  • SO4 · Sulfate ion · ion · 4 copies · chains L
  • EDO · 1,2-ethanediol · additive · 10 copies · chains L
  • ACT · Acetate ion · additive · chains L

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
12440.640.8235SO4

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

  • 4TKX · Structure of Protease · the same entry in another collection · chain L against L, TM-score 1.00
  • Q51817 · AlphaFold monomer V2.0 prediction for lys-gingipain W83 (Q51817) · a predicted model of the same protein · chain L against A, TM-score 0.98

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