GL1X · GenesisL1 explorer

MolNFT v1 · #110789 · protein

Factor xa complex with GTC000406

4Y79 · Coagulation factor X: “Factor xa complex with GTC000406”. X-ray diffraction, 3 ligands (4O6, CA, MG), 2 pockets (best druggability 0.48). MolNFT v1 #110789 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
4Y79
Type
protein
Length
287 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Coagulation factor X
EC
3.4.21.6
UniProt
P00742
Ligands
4O6, CA, MG
Pockets
2 · best druggability 0.48

Structure

x-ray diffraction · 2 distinct chains · 13% helix, 34% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ACoagulation factor X (EC 3.4.21.6)protein23413% helix, 36% strandP00742
BCoagulation factor X (EC 3.4.21.6)protein5313% helix, 26% strandP00742

Ligands and binding sites

  • 4O6 · (E)-2-(4-chlorophenyl)-N-{(3S)-1-[(2S)-1-(morpholin-4-yl)-1-oxopropan-2-yl]-2-oxopyrrolidin-3-yl}ethenesulfonamide · ligand · chains A
  • CA · Calcium ion · metal · chains A
  • MG · Magnesium ion · metal · chains A

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

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11430.480.78284O6
21840.480.7626empty

Interfaces

1 interface between chains.

  • A–B · 882 Ų buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

  • 4Y79 · Factor Xa complex with GTC000406 · the same entry in another collection · chain A against A, TM-score 1.00
  • P00742 · AlphaFold monomer V2.0 prediction for coagulation factor X (P00742) · a predicted model of the same protein · chain A against A, TM-score 0.99

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