GL1X · GenesisL1 explorer

MolNFT v1 · #111226 · protein + DNA

HNT3 in complex with DNA and guanosine

4YKL · Aprataxin-like protein: “HNT3 in complex with DNA and guanosine”. X-ray diffraction, 3 ligands (GMP, ZN, CL), 2 pockets (best druggability 0.64). MolNFT v1 #111226 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
4YKL
Type
protein + DNA
Length
205 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Aprataxin-like protein; DNA (5'-D(*GP*AP*AP*TP*CP*AP*TP*AP*AP*C)-3')
EC
3.-.-.-
UniProt
O74859
Ligands
GMP, ZN, CL
Pockets
2 · best druggability 0.64

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 18% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
BAprataxin-like protein (EC 3.-.-.-)protein19541% helix, 18% strandO74859
ADNA (5'-D(*GP*AP*AP*TP*CP*AP*TP*AP*AP*C)-3')dna10——

Ligands and binding sites

  • GMP · Guanosine · ligand · chains B, A
  • ZN · Zinc ion · metal · chains B
  • CL · Chloride ion · ion · 2 copies · chains B
  • GOL · Glycerol · additive · 4 copies · chains B, A

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

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
12310.640.8333GMP, GOL
21010.430.7716GOL

Interfaces

1 interface between chains.

  • B–A · 290 Ų buried · 3 hydrogen bonds · protein-nucleic

Compared structures

  • 4YKL · Hnt3 in complex with DNA and guanosine · the same entry in another collection · chain B against B, TM-score 1.00
  • O74859 · AlphaFold monomer V2.0 prediction for aprataxin-like protein (O74859) · a predicted model of the same protein · chain B against A, TM-score 0.99

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