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Solution structure of the DNA complex of phob DNA- BINDING/TRANSACTIVATION domain

Analyse Solution structure of the DNA complex of phob DNA- BINDING/TRANSACTIVATION… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
2Z33
Type
protein + DNA
Length
136 residues
Chains
3
Method
solution nmr
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
5'-D(*AP*CP*TP*GP*TP*CP*AP*TP*AP*AP*AP*TP*CP*TP*GP*T)-3'…
UniProt
P0AFJ5
Pockets
3 · best druggability 0.37

Structure

solution nmr · 3 distinct chains · 37% helix, 24% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
B5'-D(*AP*CP*TP*GP*TP*CP*AP*TP*AP*AP*AP*TP*CP*TP*GP*T)-3'dna16——
C5'-D(*AP*CP*AP*GP*AP*TP*TP*TP*AP*TP*GP*AP*CP*AP*GP*T)-3'dna16——
APhosphate regulon transcriptional regulatory protein phobprotein10437% helix, 24% strandP0AFJ5

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1980.370.7617empty
2690.360.7813empty
3640.270.7316empty

Interfaces

3 interfaces between chains.

  • B–C · 706 Ų buried · 47 hydrogen bonds · nucleic-nucleic
  • C–A · 468 Ų buried · 13 hydrogen bonds · protein-nucleic
  • B–A · 454 Ų buried · 10 hydrogen bonds · protein-nucleic

Compared structures

  • 2Z33 · Solution structure of the DNA complex of PhoB DNA-binding/transactivation Domain · the same entry in another collection · chain B against B, TM-score 1.00
  • P0AFJ5 · AlphaFold monomer V2.0 prediction for phosphate regulon transcriptional regulatory… · a predicted model of the same protein · chain A against A, TM-score 0.94

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