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Haddock model of MYT1 F4F5 - DNA complex

Analyse Haddock model of MYT1 F4F5 - DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
2MF8
Type
protein + DNA
Length
101 residues
Chains
3
Method
solution nmr
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Myelin transcription factor 1; DNA (5'-D(*AP*CP*CP*GP*AP*AP*AP*GP*TP*TP*CP*AP*C)-3'); DNA…
UniProt
Q8CFC2
Ligands
ZN
Pockets
2 · best druggability 0.61

Structure

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

ChainMoleculeTypeResiduesSecondary structureUniProt
AMyelin transcription factor 1protein750% helix, 0% strandQ8CFC2
BDNA (5'-D(*AP*CP*CP*GP*AP*AP*AP*GP*TP*TP*CP*AP*C)-3')dna13——
CDNA (5'-D(*GP*TP*GP*AP*AP*CP*TP*TP*TP*CP*GP*GP*T)-3')dna13——

Ligands and binding sites

  • ZN · Zinc ion · metal · 2 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
12170.610.8229empty
2720.290.7413empty

Interfaces

3 interfaces between chains.

  • B–C · 581 Ų buried · 46 hydrogen bonds · nucleic-nucleic
  • A–C · 577 Ų buried · 16 hydrogen bonds · protein-nucleic
  • A–B · 487 Ų buried · 14 hydrogen bonds · protein-nucleic

Compared structures

  • 2MF8 · HADDOCK model of MyT1 F4F5 - DNA complex · the same entry in another collection · chain A against A, TM-score 1.00
  • Q8CFC2 · AlphaFold monomer V2.0 prediction for myelin transcription factor 1 (Q8CFC2) · a predicted model of the same protein · chain A against A, TM-score 0.43

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