GL1X · GenesisL1 explorer

MolNFT v1 · #112303 · protein

Factor xa complex with GTC000102

4ZHA · Coagulation factor X: “Factor xa complex with GTC000102”. X-ray diffraction, 3 ligands (4O5, CA, MG), 2 pockets (best druggability 0.49). MolNFT v1 #112303 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
4ZHA
Type
protein
Length
286 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
4O5, CA, MG
Pockets
2 · best druggability 0.49

Structure

x-ray diffraction · 2 distinct chains · 13% helix, 36% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ACoagulation factor X (EC 3.4.21.6)protein23413% helix, 37% strandP00742
BCoagulation factor X (EC 3.4.21.6)protein5213% helix, 31% strandP00742

Ligands and binding sites

  • 4O5 · 4-[(3S)-3-({[(E)-2-(5-chlorothiophen-2-yl)ethenyl]sulfonyl}amino)-2-oxo-2,3-dihydro-1H-pyrrol-1-yl]-3-fluoro-N-methylbenzamide · 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
11390.490.79234O5
2900.370.7518empty

Interfaces

1 interface between chains.

  • A–B · 919 Ų buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

  • 4ZHA · Factor Xa complex with GTC000102 · 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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