Research workbench
NMR Structrure of d(CCAAAGXACTGGG), X is a 3'-phosphoglycolate, 5'-phosphate gapped lesion, 10 structures
Analyse NMR Structrure of d(CCAAAGXACTGGG), X is a 3'-phosphoglycolate, 5'-phosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1G5K
- Type
- DNA
- Length
- 25 nucleotides
- Chains
- 3
- Method
- solution nmr
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- NOT
- Molecule
- 5'-D(*CP*CP*AP*AP*AP*G)-3'; 5'-D(P*AP*CP*TP*GP*GP*G)-3'…
- Ligands
- PGA
Structure
solution nmr · resolution NOT · 3 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-D(*CP*CP*AP*AP*AP*G)-3' | dna | 6 | — | — |
| B | 5'-D(P*AP*CP*TP*GP*GP*G)-3' | dna | 6 | — | — |
| C | 5'-D(*CP*CP*CP*AP*GP*TP*AP*CP*TP*TP*TP*GP*G)-3' | dna | 13 | — | — |
Ligands and binding sites
- PGA · 2-phosphoglycolic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
3 interfaces between chains.
- A–C · 341 Ų buried · 35 hydrogen bonds · nucleic-nucleic
- B–C · 340 Ų buried · 34 hydrogen bonds · nucleic-nucleic
- A–B · 36 Ų buried · 0 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1G5K · NMR structrure of D(CCAAAGXACTGGG), X is a 3'-phosphoglycolate, 5'- phosphate gapped… · 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
- Elsewhere: RCSB PDB 1G5K · PDBe 1G5K
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