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Dbh ternary complex (substrates partially disordered)

Analyse Dbh ternary complex (substrates partially disordered) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
4HYK
Type
protein + DNA
Length
352 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA polymerase IV; DNA (5'-D(*GP*GP*GP*AP*AP*GP*CP*CP*GP*G)-3'); DNA (5'…
EC
2.7.7.7
UniProt
Q4JB80
Pockets
3 · best druggability 0.67

Structure

x-ray diffraction · 3 distinct chains · 42% helix, 23% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ADNA polymerase IV (EC 2.7.7.7)protein33642% helix, 23% strandQ4JB80
PDNA (5'-D(*GP*GP*GP*AP*AP*GP*CP*CP*GP*G)-3')dna8——
TDNA (5'- D(*TP*TP*CP*CP*GP*CP*CP*CP*CP*GP*GP*CP*TP*TP*CP*CP*C)-3')dna8——

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
17330.670.7659empty
23490.510.7324empty
3700.290.7316empty

Interfaces

3 interfaces between chains.

  • P–T · 350 Ų buried · 37 hydrogen bonds · nucleic-nucleic
  • A–P · 245 Ų buried · 3 hydrogen bonds · protein-nucleic
  • A–T · 140 Ų buried · 4 hydrogen bonds · protein-nucleic

Compared structures

  • 4HYK · Dbh Ternary Complex (substrates partially disordered) · the same entry in another collection · chain A against A, TM-score 1.00
  • Q4JB80 · AlphaFold monomer V2.0 prediction for DNA polymerase IV (Q4JB80) · a predicted model of the same protein · chain A against A, TM-score 0.79

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