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Crystal structure of the DNA-binding domain of human ETV1 complexed with DNA

Analyse Crystal structure of the DNA-binding domain of human ETV1 complexed with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
4BNC
Type
protein + DNA
Length
115 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Human ETV1; 5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP)-3'…
UniProt
P50549
Pockets
2 · best druggability 0.33

Structure

x-ray diffraction · 3 distinct chains · 48% helix, 13% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AHuman ETV1protein9548% helix, 13% strandP50549
B5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP)-3'dna10——
C5'-D(*CP*AP*CP*TP*TP*CP*CP*GP*GP*TP)-3'dna10——

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1960.330.7413empty
2620.320.7614empty

Interfaces

3 interfaces between chains.

  • A–C · 571 Ų buried · 8 hydrogen bonds · protein-nucleic
  • B–C · 453 Ų buried · 45 hydrogen bonds · nucleic-nucleic
  • A–B · 405 Ų buried · 9 hydrogen bonds · protein-nucleic

Compared structures

  • 4BNC · Crystal structure of the DNA-binding domain of human ETV1 complexed with DNA · the same entry in another collection · chain A against A, TM-score 1.00
  • P50549 · AlphaFold monomer V2.0 prediction for ets translocation variant 1 (P50549) · a predicted model of the same protein · chain A against A, TM-score 0.96

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