GL1X · GenesisL1 explorer

Research workbench

Crystal structure of host-guest complex with pb hachimoji DNA

Analyse Crystal structure of host-guest complex with pb hachimoji DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
6MIG
Type
protein + DNA
Length
264 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Gag-pol polyprotein; DNA (5'-D(*CP*TP*TP*AP*TP*(1WA)P*(1WA)P*(DS))-3'); DNA…
EC
3.4.23.-, 2.7.7.49, 2.7.7.7, 3.1.26.4, 2.7.7.-, 3.1.-.-
UniProt
P03355
Pockets
2 · best druggability 0.48

Structure

x-ray diffraction · 3 distinct chains · 31% helix, 25% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AGag-pol polyprotein (EC 3.4.23.-, 2.7.7.49, 2.7.7.7, 3.1.26.4, 2.7.7.-, 3.1.-.-)protein24831% helix, 25% strandP03355
BDNA (5'-D(*CP*TP*TP*AP*TP*(1WA)P*(1WA)P*(DS))-3')dna8——
GDNA (5'-D(P*(DB)P*(1W5)P*(1W5)P*AP*TP*AP*AP*G)-3')dna8——

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11740.480.7625empty
2660.370.7822empty

Interfaces

3 interfaces between chains.

  • B–G · 354 Ų buried · 33 hydrogen bonds · nucleic-nucleic
  • A–B · 230 Ų buried · 4 hydrogen bonds · protein-nucleic
  • A–G · 205 Ų buried · 4 hydrogen bonds · protein-nucleic

Modifications

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

Compared structures

  • 6MIG · Crystal structure of host-guest complex with PB hachimoji DNA · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

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