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Solution structure of a specific DNA complex of the myb DNA-binding domain with cooperative recognition helices

Analyse Solution structure of a specific DNA complex of the myb DNA-binding domain with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
1MSE
Type
protein + DNA
Length
127 residues
Chains
3
Method
solution nmr
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (5'-D(*CP*CP*TP*AP*AP*CP*TP*GP*AP*CP*AP*CP*AP*CP*AP*T)- 3'); DNA…
UniProt
P06876
Pockets
1 · best druggability 0.29

Structure

solution nmr · 3 distinct chains · 60% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ADNA (5'-D(*CP*CP*TP*AP*AP*CP*TP*GP*AP*CP*AP*CP*AP*CP*AP*T)- 3')dna11——
BDNA (5'-D(*AP*TP*GP*TP*GP*TP*GP*TP*CP*AP*GP*TP*TP*AP*GP*G)- 3')dna11——
CC-myb DNA-binding domainprotein10560% helix, 0% strandP06876

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1670.290.7413empty

Interfaces

3 interfaces between chains.

  • A–C · 798 Ų buried · 29 hydrogen bonds · protein-nucleic
  • B–C · 707 Ų buried · 18 hydrogen bonds · protein-nucleic
  • A–B · 505 Ų buried · 49 hydrogen bonds · nucleic-nucleic

Compared structures

  • 1MSE · Solution structure of a specific DNA complex of the myb DNA-binding domain with… · the same entry in another collection · chain A against A, TM-score 1.00
  • P06876 · AlphaFold monomer V2.0 prediction for transcriptional activator myb (P06876) · a predicted model of the same protein · chain C against A, TM-score 0.78

Analyse

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