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Replication of N2,3-ethenoguanine by DNA polymerases

Analyse Replication of N2,3-ethenoguanine by DNA polymerases in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
3V6J
Type
protein + DNA
Length
739 residues
Chains
6
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA polymerase IV; DNA (5'-D(*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*(DOC))-3'); DNA…
EC
2.7.7.7
UniProt
Q97W02
Ligands
DCP, MG
Pockets
5 · best druggability 0.86

Structure

x-ray diffraction · 5 distinct chains · 43% helix, 24% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A, JDNA polymerase IV (EC 2.7.7.7)protein34343% helix, 24% strandQ97W02
PDNA (5'-D(*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*(DOC))-3')dna12——
BDNA (5'-D(*TP*CP*AP*TP*(EFG) P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*C)-3')dna17——
KDNA (5'-D(*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*(DOC))-3')dna11——
MDNA (5'-D(*TP*CP*AP*TP*(EFG) P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*C)-3')dna13——

Ligands and binding sites

  • DCP · 2'-deoxycytidine-5'-triphosphate · ligand · 2 copies · chains A, P, B, J, K, M
  • MG · Magnesium ion · metal · 5 copies · chains A, J, K

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

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
110460.860.87107DCP, MG
26690.780.8366DCP, MG
35710.740.8240empty
45420.700.8039empty
51400.400.7523empty

Interfaces

7 interfaces between chains.

  • A–B · 1096 Ų buried · 27 hydrogen bonds · protein-nucleic
  • J–M · 889 Ų buried · 24 hydrogen bonds · protein-nucleic
  • A–J · 739 Ų buried · 5 hydrogen bonds · protein-protein
  • A–P · 545 Ų buried · 12 hydrogen bonds · protein-nucleic
  • J–K · 533 Ų buried · 11 hydrogen bonds · protein-nucleic

Modifications

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

Compared structures

  • 3V6J · Replication of N2,3-Ethenoguanine by DNA Polymerases · the same entry in another collection · chain M against M, 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

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