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Bypass of a bulky adduct DG1,8 by DPO4

Analyse Bypass of a bulky adduct DG1,8 by DPO4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
4RZR
Type
protein + DNA
Length
740 residues
Chains
6
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA polymerase IV; DNA (5'-D(*TP*TP*GP*C*(2JV)…
EC
2.7.7.7
UniProt
Q97W02
Ligands
2JV, DCP, CA, NA
Pockets
6 · best druggability 0.80

Structure

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

ChainMoleculeTypeResiduesSecondary structureUniProt
A, DDNA polymerase IV (EC 2.7.7.7)protein34245% helix, 25% strandQ97W02
BDNA (5'-D(*TP*TP*GP*C*(2JV) P*GP*AP*CP*TP*GP*GP*TP*AP*TP*TP*GP*GP*G)-3')dna13——
C, FDNA (5'-D(P*CP*CP*CP*AP*AP*TP*AP*CP*CP*AP*GP*TP*C)-3')dna13——
EDNA (5'-D(*TP*TP*GP*C*(2JV) P*GP*AP*CP*TP*GP*GP*TP*AP*TP*TP*GP*GP*G)-3')dna17——

Ligands and binding sites

  • 2JV · N-(8-aminopyren-1-yl)-2'-deoxy-5'-O-(trihydroxy-lambda~5~-phosphanyl)guanosine · ligand · 2 copies · chains A, B, C, D, E, F
  • DCP · 2'-deoxycytidine-5'-triphosphate · ligand · chains D, E
  • CA · Calcium ion · metal · 4 copies · chains A, C, D
  • NA · Sodium ion · metal · 2 copies · chains A, C, D, F
  • GOL · Glycerol · additive · 2 copies · chains D
  • TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B

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

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
19570.800.82692JV, CA
211060.800.8276DCP, CA, GOL
35250.730.82412JV
43180.680.8337TRS
5590.370.7912empty

Interfaces

9 interfaces between chains.

  • D–E · 1085 Ų buried · 21 hydrogen bonds · protein-nucleic
  • A–B · 752 Ų buried · 23 hydrogen bonds · protein-nucleic
  • A–C · 694 Ų buried · 19 hydrogen bonds · protein-nucleic
  • E–F · 612 Ų buried · 52 hydrogen bonds · nucleic-nucleic
  • B–C · 607 Ų buried · 51 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 3 covalent (covalent ligand).

Compared structures

  • 4RZR · Bypass of a bulky adduct dG1,8 by DPO4 · the same entry in another collection · chain F against F, 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 0.97

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