GL1X · GenesisL1 explorer

Research workbench

DPO4 extension ternary complex with OXOG(ANTI)-T(ANTI) pair

Analyse DPO4 extension ternary complex with OXOG(ANTI)-T(ANTI) pair in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
3GIL
Type
protein + DNA
Length
742 residues
Chains
6
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA polymerase IV; 5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(2DT))-3'…
EC
2.7.7.7
UniProt
Q97W02
Ligands
DGT, CA
Pockets
4 · best druggability 0.81

Structure

x-ray diffraction · 4 distinct chains · 45% helix, 25% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A, BDNA polymerase IV (EC 2.7.7.7)protein34145% helix, 25% strandQ97W02
D, H5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(2DT))-3'dna13——
E5'-D(*CP*TP*AP*AP*CP*(8OG) P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*C)-3'dna18——
J5'-D(*CP*TP*AP*AP*CP*(8OG) P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*C)-3'dna16——

Ligands and binding sites

  • DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · 2 copies · chains A, D, E, B, H, J
  • CA · Calcium ion · metal · 6 copies · chains A, B, H

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

Pockets

4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
111120.810.8379DGT, CA
211700.800.8273DGT, CA
35070.720.8147empty
46070.720.8043empty

Interfaces

7 interfaces between chains.

  • A–E · 1069 Ų buried · 26 hydrogen bonds · protein-nucleic
  • B–J · 929 Ų buried · 18 hydrogen bonds · protein-nucleic
  • B–H · 615 Ų buried · 18 hydrogen bonds · protein-nucleic
  • A–D · 574 Ų buried · 15 hydrogen bonds · protein-nucleic
  • D–E · 568 Ų buried · 43 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 4 modified (nucleotide modification).

Compared structures

  • 3GIL · Dpo4 extension ternary complex with oxoG(anti)-T(anti) pair · the same entry in another collection · chain J against J, TM-score 1.00
  • Q97W02 · AlphaFold monomer V2.0 prediction for DNA polymerase IV (Q97W02) · a predicted model of the same protein · chain A against A, TM-score 0.98

Analyse

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