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 v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.7
- Source
- Moloney murine leukemia virus (isolate Shinnick); SYNTHETIC CONSTRUCT
- 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 · resolution 1.7 · 3 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gag-Pol polyprotein (EC 3.4.23.-, 2.7.7.49, 2.7.7.7, 3.1.26.4, 2.7.7.-, 3.1.-.-) | protein | 248 | 31% helix, 25% strand | P03355 |
| B | DNA (5'-D(*CP*TP*TP*AP*TP*(1WA)P*(1WA)P*(DS))-3') | dna | 8 | — | — |
| G | DNA (5'-D(P*(DB)P*(1W5)P*(1W5)P*AP*TP*AP*AP*G)-3') | dna | 8 | — | — |
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 174 | 0.48 | 0.76 | 25 | empty |
| 2 | 66 | 0.37 | 0.78 | 22 | empty |
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
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P03355
- Elsewhere: RCSB PDB 6MIG · PDBe 6MIG · UniProt P03355
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