MolNFT v1 · #7393 · DNA
NMR structure of an oligonucleotide containing an abasic site: alpha anomer
1G5D · 5'-D(*CP*CP*AP*AP*AP*GP*(D1P)P*AP*CP*TP*GP*GP*G)-3': “NMR structure of an oligonucleotide containing an abasic site: alpha anomer”. Solution nmr, 1 ligand (ORP). MolNFT v1 #7393 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 1G5D
- Type
- DNA
- Length
- 25 nucleotides
- Chains
- 2
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*CP*AP*AP*AP*GP*(D1P)P*AP*CP*TP*GP*GP*G)-3'…
- Ligands
- ORP
Structure
solution nmr · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-D(*CP*CP*AP*AP*AP*GP*(D1P)P*AP*CP*TP*GP*GP*G)-3' | dna | 12 | — | — |
| B | 5'-D(*CP*CP*CP*AP*GP*TP*AP*CP*TP*TP*TP*GP*G)-3' | dna | 13 | — | — |
Ligands and binding sites
- ORP · 2-deoxy-5-phosphono-ribose · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
1 interface between chains.
- A–B · 668 Ų buried · 67 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1G5D · NMR structure of an oligonucleotide containing an abasic site: alpha anomer · 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 1G5D · PDBe 1G5D
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