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Structure of the R2R3 DNA binding domain of MYB1 protein from protozoan parasite trichomonas vaginalis in complex with mre-1/MRE-2R DNA

Analyse Structure of the R2R3 DNA binding domain of MYB1 protein from protozoan… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
2KDZ
Type
protein + DNA
Length
139 residues
Chains
3
Method
solution nmr
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
MYB24; 5'-D(*AP*AP*GP*AP*TP*AP*AP*CP*GP*AP*TP*AP*TP*TP*TP*A)-3'…
UniProt
Q58HP2
Pockets
4 · best druggability 0.48

Structure

solution nmr · 3 distinct chains · 56% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AMYB24protein10756% helix, 0% strandQ58HP2
B5'-D(*AP*AP*GP*AP*TP*AP*AP*CP*GP*AP*TP*AP*TP*TP*TP*A)-3'dna16——
C5'-D(*TP*AP*AP*AP*TP*AP*TP*CP*GP*TP*TP*AP*TP*CP*TP*T)-3'dna16——

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
12100.480.7523empty
2770.470.8318empty
31200.420.7714empty
41350.370.7316empty

Interfaces

3 interfaces between chains.

  • B–C · 681 Ų buried · 46 hydrogen bonds · nucleic-nucleic
  • A–B · 623 Ų buried · 27 hydrogen bonds · protein-nucleic
  • A–C · 623 Ų buried · 16 hydrogen bonds · protein-nucleic

Compared structures

  • 2KDZ · Structure of the R2R3 DNA binding domain of MYB1 protein from protozoan parasite… · the same entry in another collection · chain A against A, TM-score 1.00

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