GL1X · GenesisL1 explorer

MolNFT v1 · #153967 · protein + DNA

Rvd Q* recognizes 5HMC through water-mediated H bonds

6JW5 · Tal effector: “Rvd Q* recognizes 5HMC through water-mediated H bonds”. X-ray diffraction, 14 pockets (best druggability 0.81). MolNFT v1 #153967 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
6JW5
Type
protein + DNA
Length
2,108 residues
Chains
12
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*(5HC) P*GP*CP*GP*TP*CP*TP*CP*T)-3'); DNA…
Pockets
14 · best druggability 0.81

Structure

x-ray diffraction · 3 distinct chains · 71% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A, B, E, HTal effectorprotein49371% helix, 0% strand—
I, C, F, KDNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*(5HC) P*GP*CP*GP*TP*CP*TP*CP*T)-3')dna17——
J, D, G, LDNA (5'- D(*AP*GP*AP*GP*AP*CP*GP*CP*GP*AP*AP*GP*GP*GP*AP*CP*A)-3')dna17——

Pockets

14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
111160.810.83110empty
210780.800.82106empty
311330.790.81108empty
410970.790.8195empty
52890.510.7429empty

Interfaces

18 interfaces between chains.

  • A–I · 1734 Ų buried · 31 hydrogen bonds · protein-nucleic
  • B–C · 1718 Ų buried · 28 hydrogen bonds · protein-nucleic
  • E–F · 1712 Ų buried · 29 hydrogen bonds · protein-nucleic
  • H–K · 1682 Ų buried · 28 hydrogen bonds · protein-nucleic
  • F–G · 779 Ų buried · 74 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 4 modified (nucleotide modification).

Compared structures

  • 6JW5 · RVD Q* recognizes 5hmC through water-mediated H bonds · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

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