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NMR structure of the homeodomain transcription factor GBX1 from homo sapiens in complex with the DNA sequence cgactaattagtcg

Analyse NMR structure of the homeodomain transcription factor GBX1 from homo sapiens in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
2ME6
Type
protein + DNA
Length
99 residues
Chains
3
Method
solution nmr
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Homeobox protein gbx-1; DNA (5'-D(*CP*GP*AP*CP*TP*AP*AP*TP*TP*AP*GP*TP*CP*G)-3')
UniProt
Q14549
Pockets
1 · best druggability 0.48

Structure

solution nmr · 2 distinct chains · 52% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AHomeobox protein gbx-1protein7152% helix, 0% strandQ14549
B, CDNA (5'-D(*CP*GP*AP*CP*TP*AP*AP*TP*TP*AP*GP*TP*CP*G)-3')dna14——

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1920.480.8215empty

Interfaces

3 interfaces between chains.

  • B–C · 655 Ų buried · 49 hydrogen bonds · nucleic-nucleic
  • A–B · 647 Ų buried · 24 hydrogen bonds · protein-nucleic
  • A–C · 571 Ų buried · 16 hydrogen bonds · protein-nucleic

Compared structures

  • 2ME6 · NMR Structure of the homeodomain transcription factor Gbx1 from Homo sapiens in complex… · the same entry in another collection · chain A against A, TM-score 1.00
  • Q14549 · AlphaFold monomer V2.0 prediction for homeobox protein gbx-1 (Q14549) · a predicted model of the same protein · chain A against A, TM-score 0.58

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