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MolNFT v1 · #156777 · protein

Improved model of human coagulation factor VIII

6MF2: “Improved model of human coagulation factor VIII”. X-ray diffraction, 5 ligands (NAG, BMA, CA), 17 pockets (best druggability 0.85). MolNFT v1 #156777 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
6MF2
Type
protein
Length
1,222 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Coagulation factor VIII
UniProt
P00451
Ligands
NAG, BMA, CA, ZN, CU1
Pockets
17 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 6% helix, 32% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ACoagulation factor VIIIprotein12226% helix, 32% strandP00451

Ligands and binding sites

  • NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A
  • BMA · beta-D-mannopyranose · sugar · 3 copies
  • CA · Calcium ion · metal · chains A
  • ZN · Zinc ion · metal · chains A
  • CU1 · Copper (I) ion · metal · chains A

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

Pockets

17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
15820.850.9050empty
210330.770.7985NAG
33250.710.8453empty
45530.680.7853empty
5560.650.9522empty

Modifications

Observed in the structure: 7 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

  • 6MF2 · Improved Model of Human Coagulation Factor VIII · the same entry in another collection · chain A against A, TM-score 1.00
  • P00451 · AlphaFold monomer V2.0 prediction for coagulation factor VIII (P00451) · a predicted model of the same protein · chain A against A, TM-score 0.99

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