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NMR solution structure of the extended pbx homeodomain bound to DNA

Analyse NMR solution structure of the extended pbx homeodomain 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
1LFU
Type
protein + DNA
Length
110 residues
Chains
3
Method
solution nmr
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
5'-D(*GP*CP*GP*CP*AP*TP*GP*AP*TP*TP*GP*CP*CP*C)-3'…
UniProt
P41778
Pockets
2 · best druggability 0.45

Structure

solution nmr · 3 distinct chains · 63% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A5'-D(*GP*CP*GP*CP*AP*TP*GP*AP*TP*TP*GP*CP*CP*C)-3'dna14——
B5'-D(*GP*GP*GP*CP*AP*AP*TP*CP*AP*TP*GP*CP*GP*C)-3'dna14——
PHomeobox protein PBX1protein8263% helix, 0% strandP41778

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1810.450.8116empty
2660.290.7415empty

Interfaces

3 interfaces between chains.

  • A–B · 636 Ų buried · 51 hydrogen bonds · nucleic-nucleic
  • B–P · 572 Ų buried · 9 hydrogen bonds · protein-nucleic
  • A–P · 501 Ų buried · 10 hydrogen bonds · protein-nucleic

Compared structures

  • 1LFU · NMR Solution Structure of the Extended PBX Homeodomain Bound to DNA · the same entry in another collection · chain A against A, TM-score 1.00
  • P41778 · AlphaFold monomer V2.0 prediction for pre-B-cell leukemia transcription factor 1 (P41778) · a predicted model of the same protein · chain P against A, TM-score 0.70

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