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High resolution crystal structure of DNA APURINIC/APYRIMIDINIC (ap) endonuclease IV nfo from thermatoga maritima

Analyse High resolution crystal structure of DNA APURINIC/APYRIMIDINIC (ap)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
4HNO
Type
protein
Length
285 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Probable endonuclease 4
EC
3.1.21.2
UniProt
Q9WYJ7
Ligands
ZN, MN, MG, SO4
Pockets
1 · best druggability 0.42

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 15% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AProbable endonuclease 4 (EC 3.1.21.2)protein28545% helix, 15% strandQ9WYJ7

Ligands and binding sites

  • ZN · Zinc ion · metal · 3 copies · chains A
  • MN · Manganese (II) ion · metal · 2 copies · chains A
  • MG · Magnesium ion · metal
  • SO4 · Sulfate ion · ion · chains A
  • EDO · 1,2-ethanediol · additive · 2 copies · chains A
  • TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A

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

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1960.420.7821empty

Compared structures

  • 4HNO · High resolution crystal structure of DNA Apurinic/apyrimidinic (AP) endonuclease IV Nfo… · the same entry in another collection · chain A against A, TM-score 1.00
  • Q9WYJ7 · AlphaFold monomer V2.0 prediction for probable endonuclease 4 (Q9WYJ7) · a predicted model of the same protein · chain A against A, TM-score 0.99

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