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VND/NK-2 HOMEODOMAIN/DNA complex, NMR, minimized average structure

Analyse VND/NK-2 HOMEODOMAIN/DNA complex, NMR, minimized average structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
1NK3
Type
protein + DNA
Length
95 residues
Chains
3
Method
solution nmr
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (5'-D(*TP*GP*TP*GP*TP*CP*AP*AP*GP*TP*GP*GP*CP*TP*GP*T)- 3'); DNA…
UniProt
P22808
Pockets
1 · best druggability 0.47

Structure

solution nmr · 3 distinct chains · 70% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ADNA (5'-D(*TP*GP*TP*GP*TP*CP*AP*AP*GP*TP*GP*GP*CP*TP*GP*T)- 3')dna16——
BDNA (5'-D(*AP*CP*AP*GP*CP*CP*AP*CP*TP*TP*GP*AP*CP*AP*CP*A)- 3')dna16——
PHomeobox protein vndprotein6370% helix, 0% strandP22808

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11300.470.7817empty

Interfaces

3 interfaces between chains.

  • A–B · 719 Ų buried · 63 hydrogen bonds · nucleic-nucleic
  • B–P · 519 Ų buried · 13 hydrogen bonds · protein-nucleic
  • A–P · 438 Ų buried · 6 hydrogen bonds · protein-nucleic

Compared structures

  • 1NK3 · VND/NK-2 HOMEODOMAIN/DNA complex, NMR, minimized average structure · the same entry in another collection · chain A against A, TM-score 1.00
  • P22808 · AlphaFold monomer V2.0 prediction for homeobox protein vnd (P22808) · a predicted model of the same protein · chain P against A, TM-score 0.86

Analyse

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