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MolNFT v1 · #81910 · protein + DNA

Replication of N2,3-ethenoguanine by DNA polymerases

3V6K · DNA polymerase IV: “Replication of N2,3-ethenoguanine by DNA polymerases”. X-ray diffraction, 3 ligands (CA, MG, NA), 10 pockets (best druggability 0.82). MolNFT v1 #81910 on GenesisL1: 3D structure, binding sites and pockets in…

PDB
3V6K
Type
protein + DNA
Length
722 residues
Chains
6
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA polymerase IV; DNA (5'-D(P*GP*AP*AP*GP*GP*AP*TP*TP*CP*(2DT))-3'); DNA…
EC
2.7.7.7
UniProt
Q97W02
Ligands
CA, MG, NA
Pockets
10 · best druggability 0.82

Structure

x-ray diffraction · 5 distinct chains · 41% helix, 22% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ADNA polymerase IV (EC 2.7.7.7)protein34242% helix, 23% strandQ97W02
JDNA polymerase IV (EC 2.7.7.7)protein33339% helix, 21% strandQ97W02
P, KDNA (5'-D(P*GP*AP*AP*GP*GP*AP*TP*TP*CP*(2DT))-3')dna10——
BDNA (5'-D(*TP*CP*AP*CP*(EFG)P*GP*AP*AP*TP*CP*CP*TP*TP*C)- 3')dna14——
MDNA (5'-D(*TP*CP*AP*CP*(EFG)P*GP*AP*AP*TP*CP*CP*TP*TP*C)- 3')dna13——

Ligands and binding sites

  • CA · Calcium ion · metal · 7 copies · chains A, P, J, K
  • MG · Magnesium ion · metal · 4 copies · chains A, P, J, K
  • NA · Sodium ion · metal · 4 copies · chains P, B

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

Pockets

10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
19740.820.8496MG, CA
29050.820.8466MG
34510.720.8245empty
45000.710.8142empty
53380.670.8150empty

Interfaces

7 interfaces between chains.

  • A–B · 1067 Ų buried · 17 hydrogen bonds · protein-nucleic
  • J–M · 847 Ų buried · 15 hydrogen bonds · protein-nucleic
  • J–K · 695 Ų buried · 16 hydrogen bonds · protein-nucleic
  • A–P · 674 Ų buried · 14 hydrogen bonds · protein-nucleic
  • A–J · 573 Ų buried · 4 hydrogen bonds · protein-protein

Modifications

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

Compared structures

  • 3V6K · 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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