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Solution NMR-derived complex structure of HOXA13 DNA binding domain bound to DNA

Analyse Solution NMR-derived complex structure of HOXA13 DNA binding domain bound to DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
2LD5
Type
protein + DNA
Length
89 residues
Chains
3
Method
solution nmr
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Homeobox protein hox-A13; DNA (5'-D(*CP*AP*AP*AP*TP*AP*AP*AP*AP*TP*C)-3'); DNA…
UniProt
Q62424
Pockets
1 · best druggability 0.30

Structure

solution nmr · 3 distinct chains · 66% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AHomeobox protein hox-A13protein6766% helix, 0% strandQ62424
BDNA (5'-D(*CP*AP*AP*AP*TP*AP*AP*AP*AP*TP*C)-3')dna11——
CDNA (5'-D(P*GP*AP*TP*TP*TP*TP*AP*TP*TP*TP*G)-3')dna11——

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1630.300.7512empty

Interfaces

3 interfaces between chains.

  • A–C · 796 Ų buried · 26 hydrogen bonds · protein-nucleic
  • A–B · 642 Ų buried · 16 hydrogen bonds · protein-nucleic
  • B–C · 511 Ų buried · 38 hydrogen bonds · nucleic-nucleic

Compared structures

  • 2LD5 · Solution NMR-derived complex structure of Hoxa13 DNA binding domain bound to DNA · the same entry in another collection · chain A against A, TM-score 1.00
  • Q62424 · AlphaFold monomer V2.0 prediction for homeobox protein hox-A13 (Q62424) · a predicted model of the same protein · chain A against A, TM-score 0.68

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