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Human aprataxin (aptx) H201Q bound to RNA-DNA, AMP and zn product complex

Analyse Human aprataxin (aptx) H201Q bound to RNA-DNA, AMP and zn product complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
6CVQ
Type
protein + DNA
Length
400 residues
Chains
6
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Aprataxin; DNA/RNA (5'-R(P*G)-D(P*TP*TP*AP*TP*GP*AP*TP*TP*C)-3'); DNA…
EC
3.1.11.7, 3.1.12.2
UniProt
Q7Z2E3
Ligands
AMP, ZN, NA
Pockets
7 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 37% helix, 17% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A, BAprataxin (EC 3.1.11.7, 3.1.12.2)protein18037% helix, 17% strandQ7Z2E3
D, GDNA/RNA (5'-R(P*G)-D(P*TP*TP*AP*TP*GP*AP*TP*TP*C)-3')dna10——
E, HDNA (5'-D(*GP*AP*AP*TP*CP*AP*TP*AP*AP*C)-3')dna10——

Ligands and binding sites

  • AMP · Adenosine monophosphate · ligand · 2 copies · chains A, D, B, G
  • ZN · Zinc ion · metal · 2 copies · chains A, B
  • NA · Sodium ion · metal · chains A, D
  • BME · Beta-mercaptoethanol · additive · 2 copies · chains A, D, B, G
  • GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
17030.750.8063AMP
26330.670.7748NA
31370.650.8725AMP
44940.610.7536empty
51040.480.8018empty

Interfaces

9 interfaces between chains.

  • G–H · 409 Ų buried · 30 hydrogen bonds · nucleic-nucleic
  • D–E · 394 Ų buried · 28 hydrogen bonds · nucleic-nucleic
  • A–B · 373 Ų buried · 3 hydrogen bonds · protein-protein
  • A–D · 365 Ų buried · 5 hydrogen bonds · protein-nucleic
  • B–G · 355 Ų buried · 8 hydrogen bonds · protein-nucleic

Compared structures

  • 6CVQ · Human Aprataxin (Aptx) H201Q bound to RNA-DNA, AMP and Zn product complex · the same entry in another collection · chain H against H, TM-score 1.00
  • Q7Z2E3 · AlphaFold monomer V2.0 prediction for aprataxin (Q7Z2E3) · a predicted model of the same protein · chain B against A, TM-score 0.98

Analyse

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