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Dethiobiotin synthetase complexed with 7-(carboxyamino)-8- amino-nonanoic acid, ADP, and calcium

Analyse Dethiobiotin synthetase complexed with 7-(carboxyamino)-8- amino-nonanoic acid… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
1DAF
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
DSD, ADP, CA
Pockets
1 · best druggability 0.46

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 22% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ADethiobiotin synthetase (EC 6.3.3.3)protein22438% helix, 22% strandP13000

Ligands and binding sites

  • DSD · 7-(carboxyamino)-8-amino-nonanoic acid · ligand · chains A
  • ADP · Adenosine-5'-diphosphate · ligand · chains A
  • CA · Calcium ion · metal · 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
11490.460.7732DSD, ADP

Compared structures

  • 1DAF · Dethiobiotin synthetase complexed with 7-(carboxyamino)-8-amino-nonanoic acid, 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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