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Crystal structure of host-guest complex with pp hachimoji DNA

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

PDB
6MIK
Type
protein + DNA
Length
264 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
N-terminal fragment of mmlv reverse transcriptase; 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
1 · best druggability 0.48

Structure

x-ray diffraction · 3 distinct chains · 31% helix, 24% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AN-terminal fragment of mmlv reverse transcriptase (EC 3.4.23.-, 2.7.7.49, 2.7.7.7, 3.1.26.4, 2.7.7.-, 3.1.-.-)protein24831% helix, 24% 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

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11700.480.7627empty

Interfaces

3 interfaces between chains.

  • B–G · 362 Ų buried · 33 hydrogen bonds · nucleic-nucleic
  • A–B · 227 Ų buried · 4 hydrogen bonds · protein-nucleic
  • A–G · 209 Ų buried · 4 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 6 modified (nucleotide modification).

Compared structures

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

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