GL1X · GenesisL1 explorer

Research workbench

Helicase substrate complex

Analyse Helicase substrate complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
3PJR
Type
protein + DNA
Length
671 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
5'-D(*GP*CP*AP*GP*TP*GP*CP*TP*CP*GP*TP*TP*TP*TP*T)-3'…
EC
3.6.1.-
UniProt
P56255
Ligands
ATP
Pockets
9 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 48% helix, 11% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
Y5'-D(*GP*CP*AP*GP*TP*GP*CP*TP*CP*GP*TP*TP*TP*TP*T)-3'dna15——
Z5'-D(*CP*GP*AP*GP*CP*AP*CP*TP*GP*C)-3'dna10——
AHelicase pcra (EC 3.6.1.-)protein64648% helix, 11% strandP56255

Ligands and binding sites

  • ATP · Adenosine-5'-triphosphate · ligand · chains A

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

Pockets

9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
111540.770.7993empty
27320.730.7960empty
34180.690.8155ATP
43450.660.8138empty
52460.550.7722empty

Interfaces

3 interfaces between chains.

  • Y–A · 894 Ų buried · 16 hydrogen bonds · protein-nucleic
  • Y–Z · 438 Ų buried · 23 hydrogen bonds · nucleic-nucleic
  • Z–A · 41 Ų buried · 0 hydrogen bonds · protein-nucleic

Compared structures

  • 3PJR · Helicase substrate complex · the same entry in another collection · chain Y against Y, TM-score 1.00
  • P56255 · AlphaFold monomer V2.0 prediction for ATP-dependent DNA helicase pcra (P56255) · a predicted model of the same protein · chain A against A, TM-score 0.95

Analyse

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.