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Ternary complex of sulfolobus solfataricus DPO4 DNA polymerase, 7,8-dihydro-8-oxodeoxyguanine modified DNA and dctp - magnesium form

Analyse Ternary complex of sulfolobus solfataricus DPO4 DNA polymerase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
2XCP
Type
protein + DNA
Length
743 residues
Chains
6
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA polymerase IV; 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP *TP*DOC)-3'…
EC
2.7.7.7
UniProt
Q97W02
Ligands
DCP, MG
Pockets
5 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 41% helix, 24% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ADNA polymerase IV (EC 2.7.7.7)protein34144% helix, 24% strandQ97W02
BDNA polymerase IV (EC 2.7.7.7)protein34238% helix, 24% strandQ97W02
E, P5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP *TP*DOC)-3'dna13——
F, T5'-D(*TP*CP*AP*CP*8OGP*GP*AP*AP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3'dna17——

Ligands and binding sites

  • DCP · 2'-deoxycytidine-5'-triphosphate · ligand · 2 copies · chains A, P, T, B, E, F
  • MG · Magnesium ion · metal · 6 copies · chains A, B, P, E

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
111350.790.8178MG, DCP
211680.790.8179MG, DCP
35240.740.8342empty
46500.740.8147empty
5600.280.7412empty

Interfaces

8 interfaces between chains.

  • B–F · 1014 Ų buried · 23 hydrogen bonds · protein-nucleic
  • A–T · 962 Ų buried · 24 hydrogen bonds · protein-nucleic
  • A–P · 592 Ų buried · 14 hydrogen bonds · protein-nucleic
  • B–E · 574 Ų buried · 15 hydrogen bonds · protein-nucleic
  • E–F · 565 Ų buried · 53 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

  • 2XCP · TERNARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE, 7,8… · the same entry in another collection · chain T against T, 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 0.99

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