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The monomer mutant of BEN4 domain of protein BEND3 with DNA

Analyse The monomer mutant of BEN4 domain of protein BEND3 with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
7V9I
Type
protein + DNA
Length
129 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Ben domain-containing protein 3; DNA (5'-D(*GP*CP*CP*CP*CP*AP*CP*GP*CP*GP*GP*T)-3'); DNA…
UniProt
Q6PAL0
Pockets
2 · best druggability 0.54

Structure

x-ray diffraction · 3 distinct chains · 64% helix, 4% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ABen domain-containing protein 3protein10564% helix, 4% strandQ6PAL0
BDNA (5'-D(*GP*CP*CP*CP*CP*AP*CP*GP*CP*GP*GP*T)-3')dna12——
CDNA (5'-D(*AP*CP*CP*GP*CP*GP*TP*GP*GP*GP*GP*C)-3')dna12——

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
12000.540.7923empty
21130.440.7826empty

Interfaces

3 interfaces between chains.

  • A–C · 582 Ų buried · 9 hydrogen bonds · protein-nucleic
  • B–C · 545 Ų buried · 42 hydrogen bonds · nucleic-nucleic
  • A–B · 344 Ų buried · 6 hydrogen bonds · protein-nucleic

Compared structures

  • 7V9I · The Monomer mutant of BEN4 domain of protein Bend3 with DNA · the same entry in another collection · chain A against A, TM-score 1.00
  • Q6PAL0 · AlphaFold monomer V2.0 prediction for ben domain-containing protein 3 (Q6PAL0) · a predicted model of the same protein · chain A against A, TM-score 0.85

Analyse

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