Research workbench
One sugar pucker fits all: pairing versatility despite conformational uniformity in tna
Analyse One sugar pucker fits all: pairing versatility despite conformational… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PWF
- Type
- DNA
- Length
- 20 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*CP*GP*TP*AP*(2MU)P*(FA2)P*CP*GP*C)-3'
- Ligands
- SPM
- Pockets
- 1 · best druggability 0.21
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 5'-D(*GP*CP*GP*TP*AP*(2MU)P*(FA2)P*CP*GP*C)-3' | dna | 10 | — | — |
Ligands and binding sites
- SPM · Spermine · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.21 | 0.71 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 485 Ų buried · 40 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 1PWF · One Sugar Pucker Fits All: Pairing Versatility Despite Conformational Uniformity in TNA · 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 1PWF · PDBe 1PWF
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