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Structure of a NDT80-DNA complex (mse variant VA4G)

Analyse Structure of a NDT80-DNA complex (mse variant VA4G) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
2EUX
Type
protein + DNA
Length
318 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
5'-D(*TP*GP*CP*GP*AP*CP*GP*CP*AP*AP*AP*AP*AP*C)-3'…
UniProt
P38830
Pockets
4 · best druggability 0.69

Structure

x-ray diffraction · 3 distinct chains · 16% helix, 41% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
B5'-D(*TP*GP*CP*GP*AP*CP*GP*CP*AP*AP*AP*AP*AP*C)-3'dna14——
C5'-D(*AP*GP*TP*TP*TP*TP*TP*GP*CP*GP*TP*CP*GP*C)-3'dna14——
ANDT80 proteinprotein29016% helix, 41% strandP38830

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
12870.690.8431empty
22060.470.7433empty
3650.370.7914empty
4530.300.7615empty

Interfaces

3 interfaces between chains.

  • C–A · 829 Ų buried · 20 hydrogen bonds · protein-nucleic
  • B–A · 688 Ų buried · 13 hydrogen bonds · protein-nucleic
  • B–C · 602 Ų buried · 44 hydrogen bonds · nucleic-nucleic

Compared structures

  • 2EUX · Structure of a Ndt80-DNA complex (MSE VARIANT vA4G) · the same entry in another collection · chain B against B, TM-score 1.00
  • P38830 · AlphaFold monomer V2.0 prediction for meiosis-specific transcription factor NDT80 (P38830) · a predicted model of the same protein · chain A against A, TM-score 1.00

Analyse

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