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Factor xa specific inhibitor in complex with rat trypsin mutant X99/175/190RT

Analyse Factor xa specific inhibitor in complex with rat trypsin mutant X99/175/190RT in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
1J17
Type
protein
Length
223 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Trypsin II, anionic
EC
3.4.21.4
UniProt
P00763
Ligands
ZEN, CA, SO4
Pockets
1 · best druggability 0.39

Structure

x-ray diffraction · 1 distinct chain · 10% helix, 36% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
TTrypsin II, anionic (EC 3.4.21.4)protein22310% helix, 36% strandP00763

Ligands and binding sites

  • ZEN · [4-(6-chloro-naphthalene-2-sulfonyl)-piperazin-1-yl]- (3,4,5,6-tetrahydro-2H-[1,4']bipyridinyl-4-yl)- methanone · ligand · chains T
  • CA · Calcium ion · metal · chains T
  • SO4 · Sulfate ion · ion · chains T

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1510.390.8116SO4

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

  • 1J17 · Factor xa specific inhibitor in complex with rat trypsin mutant X99/175/190RT · the same entry in another collection · chain T against T, TM-score 1.00
  • P00763 · AlphaFold monomer V2.0 prediction for anionic trypsin-2 (P00763) · a predicted model of the same protein · chain T against A, TM-score 0.99

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