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Crystal structure of D181A/R192F HFEN1 in complex with DNA

Analyse Crystal structure of D181A/R192F HFEN1 in complex with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
5ZOF
Type
protein + DNA
Length
330 residues
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Flap endonuclease 1; DNA (5'- D(*CP*CP*TP*CP*TP*GP*CP*CP*TP*CP*AP*AP*GP*AP*CP*GP*GP*G)-3')…
EC
3.1.-.-
UniProt
P39748
Ligands
K
Pockets
1 · best druggability 0.75

Structure

x-ray diffraction · 4 distinct chains · 51% helix, 12% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AFlap endonuclease 1 (EC 3.1.-.-)protein29051% helix, 12% strandP39748
BDNA (5'- D(*CP*CP*TP*CP*TP*GP*CP*CP*TP*CP*AP*AP*GP*AP*CP*GP*GP*G)-3')dna18——
CDNA (5'-D(*GP*CP*CP*CP*GP*TP*CP*C)-3')dna8——
DDNA (5'-D(*AP*CP*TP*TP*TP*GP*AP*GP*GP*CP*AP*GP*AP*G)-3')dna14——

Ligands and binding sites

  • K · Potassium ion · metal · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
19460.750.7882empty

Interfaces

5 interfaces between chains.

  • A–B · 696 Ų buried · 14 hydrogen bonds · protein-nucleic
  • B–D · 551 Ų buried · 44 hydrogen bonds · nucleic-nucleic
  • A–C · 373 Ų buried · 6 hydrogen bonds · protein-nucleic
  • B–C · 293 Ų buried · 31 hydrogen bonds · nucleic-nucleic
  • A–D · 230 Ų buried · 0 hydrogen bonds · protein-nucleic

Compared structures

  • 5ZOF · Crystal Structure of D181A/R192F hFen1 in complex with DNA · the same entry in another collection · chain A against A, TM-score 1.00
  • P39748 · AlphaFold monomer V2.0 prediction for flap endonuclease 1 (P39748) · a predicted model of the same protein · chain A against A, TM-score 0.97

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