MolNFT v1 · #7847 · DNA
NMR structure of D(CCAAAGXACTGGG), X is a 3'PHOSPHOGLYCOLATE, 5'PHOSPHATE gapped lesion
1GJ1 · 5'-D(*CP*CP*AP*AP*AP*G)-3': “NMR structure of D(CCAAAGXACTGGG), X is a 3'PHOSPHOGLYCOLATE, 5'PHOSPHATE gapped lesion”. Solution nmr, 1 ligand (PGA). MolNFT v1 #7847 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1GJ1
- Type
- DNA
- Length
- 25 nucleotides
- Chains
- 3
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- 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 · 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.
- B–C · 341 Ų buried · 36 hydrogen bonds · nucleic-nucleic
- A–C · 324 Ų buried · 35 hydrogen bonds · nucleic-nucleic
- A–B · 42 Ų buried · 0 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1GJ1 · NMR structure of d(CCAAAGXACTGGG), X is a 3'phosphoglycolate, 5'phosphate gapped lesion · 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 1GJ1 · PDBe 1GJ1
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