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Structural basis for nucleic acid and toxin recognition of the bacterial antitoxin ccda

Analyse Structural basis for nucleic acid and toxin recognition of the bacterial… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
2H3A
Type
protein + DNA
Length
170 residues
Chains
4
Method
solution nmr
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
5'-D(P*AP*TP*AP*TP*GP*TP*AP*TP*AP*CP*CP*CP*G)-3'…
UniProt
Q9S0Z5
Pockets
3 · best druggability 0.55

Structure

solution nmr · 3 distinct chains · 29% helix, 8% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
C5'-D(P*AP*TP*AP*TP*GP*TP*AP*TP*AP*CP*CP*CP*G)-3'dna13——
D5'-D(P*TP*CP*GP*GP*GP*TP*AP*TP*AP*CP*AP*TP*A)-3'dna13——
A, BCcdaprotein7229% helix, 8% strandQ9S0Z5

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
13000.550.7530empty
2770.330.7523empty
3650.320.7614empty

Interfaces

6 interfaces between chains.

  • A–B · 1815 Ų buried · 25 hydrogen bonds · protein-protein
  • D–B · 675 Ų buried · 20 hydrogen bonds · protein-nucleic
  • C–D · 639 Ų buried · 67 hydrogen bonds · nucleic-nucleic
  • C–B · 502 Ų buried · 11 hydrogen bonds · protein-nucleic
  • D–A · 302 Ų buried · 7 hydrogen bonds · protein-nucleic

Compared structures

  • 2H3A · Structural basis for nucleic acid and toxin recognition of the bacterial antitoxin CcdA · the same entry in another collection · chain C against C, TM-score 1.00

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