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MolNFT v1 · #4021 · protein

Dethiobiotin synthetase from escherichia COLI, complex reaction intermediate ADP and mixed anhydride

1DAK: “Dethiobiotin synthetase from escherichia COLI, complex reaction intermediate ADP and mixed anhydride”. X-ray diffraction, 4 ligands (DPU, ADP, MG), 1 pocket (best druggability 0.48). MolNFT v1 #4021 on GenesisL1: 3D structure…

PDB
1DAK
Type
protein
Length
224 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Dethiobiotin synthetase
EC
6.3.3.3
UniProt
P13000
Ligands
DPU, ADP, MG, PO4
Pockets
1 · best druggability 0.48

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 21% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ADethiobiotin synthetase (EC 6.3.3.3)protein22439% helix, 21% strandP13000

Ligands and binding sites

  • DPU · Mixed carbamic phosphoric acid anhydride of 7,8-diaminononanic acid · ligand · chains A
  • ADP · Adenosine-5'-diphosphate · ligand · chains A
  • MG · Magnesium ion · metal · 2 copies · chains A
  • PO4 · Phosphate ion · ion · chains A

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
11790.480.7632MG, DPU, ADP

Compared structures

  • 1DAK · Dethiobiotin synthetase from escherichia COLI, complex reaction intermediate ADP and… · the same entry in another collection · chain A against A, TM-score 1.00
  • P13000 · AlphaFold monomer V2.0 prediction for ATP-dependent dethiobiotin synthetase biod 1… · a predicted model of the same protein · chain A against A, TM-score 0.99

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