Research workbench
Structure of an RNA-2'-deoxyguanosine complex
Analyse Structure of an RNA-2'-deoxyguanosine complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DS7
- Type
- RNA
- Length
- 134 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 67-mer
- Ligands
- NCO, GNG
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 67-mer | rna | 67 | — | — |
Ligands and binding sites
- NCO · Cobalt hexammine(iii) · ligand · 11 copies · chains A, B
- GNG · 2'-deoxy-guanosine · ligand · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1074 | 0.76 | 0.80 | 56 | GNG, NCO, ACT |
| 2 | 1053 | 0.76 | 0.79 | 53 | GNG, NCO, ACT |
| 3 | 200 | 0.47 | 0.76 | 18 | empty |
| 4 | 230 | 0.43 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 313 Ų buried · 7 hydrogen bonds · nucleic-nucleic
Compared structures
- 3DS7 · Structure of an RNA-2'-deoxyguanosine complex · the same entry in another collection · chain B against B, 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 3DS7 · PDBe 3DS7
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