GL1X · GenesisL1 explorer

MolNFT v1 · #153962 · protein + DNA

Universal rvd R* accommodates cytosine via water-mediated interactions

6JW0 · Tal effector: “Universal rvd R* accommodates cytosine via water-mediated interactions”. X-ray diffraction, 7 pockets (best druggability 0.80). MolNFT v1 #153962 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
6JW0
Type
protein + DNA
Length
1,060 residues
Chains
6
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Tal effector; DNA (5'- D(*TP*GP*TP*CP*CP*CP*TP*TP*CP*GP*CP*GP*TP*CP*TP*CP*T)-3'); DNA…
Pockets
7 · best druggability 0.80

Structure

x-ray diffraction · 3 distinct chains · 74% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A, BTal effectorprotein49674% helix, 0% strand—
I, CDNA (5'- D(*TP*GP*TP*CP*CP*CP*TP*TP*CP*GP*CP*GP*TP*CP*TP*CP*T)-3')dna17——
J, DDNA (5'- D(*AP*GP*AP*GP*AP*CP*GP*CP*GP*AP*AP*GP*GP*GP*AP*CP*A)-3')dna17——

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
111310.800.82126empty
210860.790.81114empty
32190.410.7225empty
4540.360.7912empty
51080.330.7219empty

Interfaces

11 interfaces between chains.

  • B–C · 1759 Ų buried · 26 hydrogen bonds · protein-nucleic
  • A–I · 1744 Ų buried · 25 hydrogen bonds · protein-nucleic
  • I–J · 761 Ų buried · 68 hydrogen bonds · nucleic-nucleic
  • C–D · 745 Ų buried · 62 hydrogen bonds · nucleic-nucleic
  • A–B · 723 Ų buried · 6 hydrogen bonds · protein-protein

Compared structures

  • 6JW0 · Universal RVD R* accommodates cytosine via water-mediated interactions · the same entry in another collection · chain A against A, TM-score 1.00

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