GL1X · GenesisL1 explorer

MolNFT v1 · #102418 · protein + DNA + RNA

TY3 reverse transcriptase bound to DNA/RNA

4OL8 · Reverse TRANSCRIPTASE/RIBONUCLEASE H: “TY3 reverse transcriptase bound to DNA/RNA”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.84). MolNFT v1 #102418 on GenesisL1: 3D structure, binding sites and pockets in…

PDB
4OL8
Type
protein + DNA + RNA
Length
1,715 residues
Chains
8
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Reverse TRANSCRIPTASE/RIBONUCLEASE H; 5'-R(*CP*UP*GP*AP*GP*AP*GP*AP*GP*AP*GP*GP*AP*AP*GP*A…
EC
2.7.7.49, 2.7.7.7, 3.1.26.4
UniProt
Q99315
Ligands
SO4
Pockets
20 · best druggability 0.84

Structure

x-ray diffraction · 7 distinct chains · 33% helix, 20% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AReverse TRANSCRIPTASE/RIBONUCLEASE H (EC 2.7.7.49, 2.7.7.7, 3.1.26.4)protein39033% helix, 20% strandQ99315
BReverse TRANSCRIPTASE/RIBONUCLEASE H (EC 2.7.7.49, 2.7.7.7, 3.1.26.4)protein45236% helix, 21% strandQ99315
C, G5'-R(*CP*UP*GP*AP*GP*AP*GP*AP*GP*AP*GP*GP*AP*AP*GP*AP*UP*G) -3'rna17——
D5'-D(*CP*AP*TP*CP*TP*TP*CP*CP*TP*CP*TP*CP*TP*CP*TP*C)-3'dna15——
H5'-D(*CP*AP*TP*CP*TP*TP*CP*CP*TP*CP*TP*CP*TP*CP*TP*C)-3'dna16——
FReverse TRANSCRIPTASE/RIBONUCLEASE H (EC 2.7.7.49, 2.7.7.7, 3.1.26.4)protein42731% helix, 23% strandQ99315
EReverse TRANSCRIPTASE/RIBONUCLEASE H (EC 2.7.7.49, 2.7.7.7, 3.1.26.4)protein38129% helix, 17% strandQ99315

Ligands and binding sites

  • SO4 · Sulfate ion · ion · 2 copies · chains B

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

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
111700.840.85129empty
26010.830.8870empty
310270.760.7892empty
44780.740.8355empty
55200.660.7851empty

Interfaces

16 interfaces between chains.

  • F–E · 1343 Ų buried · 16 hydrogen bonds · protein-protein
  • A–B · 1339 Ų buried · 17 hydrogen bonds · protein-protein
  • G–H · 780 Ų buried · 80 hydrogen bonds · nucleic-nucleic
  • C–D · 747 Ų buried · 68 hydrogen bonds · nucleic-nucleic
  • A–D · 693 Ų buried · 6 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 20 modified (engineered).

Compared structures

  • 4OL8 · Ty3 reverse transcriptase bound to DNA/RNA · the same entry in another collection · chain E against E, TM-score 1.00
  • Q99315 · AlphaFold monomer V2.0 prediction for transposon TY3-G gag-pol polyprotein (Q99315) · a predicted model of the same protein · chain B against A, TM-score 0.99

Analyse

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.