Research workbench
Crystal structure of a self-assembling DNA scaffold containing ta sticky ends and rhombohedral symmetry
Analyse Crystal structure of a self-assembling DNA scaffold containing ta sticky ends… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UDN
- Type
- DNA
- Length
- 42 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*TP*AP*CP*TP*GP*AP*CP*TP*CP*AP*TP*GP*CP*TP*CP*AP*TP*CP*TP*GP*A)- 3'); DNA…
- Ligands
- ARS
Structure
x-ray diffraction · 4 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA (5'- D(*TP*AP*CP*TP*GP*AP*CP*TP*CP*AP*TP*GP*CP*TP*CP*AP*TP*CP*TP*GP*A)- 3') | dna | 21 | — | — |
| A | DNA (5'-D(P*AP*GP*CP*AP*TP*GP*A)-3') | dna | 7 | — | — |
| C | DNA (5'-D(*TP*AP*TP*CP*AP*GP*AP*TP*G)-3') | dna | 9 | — | — |
| D | DNA (5'-D(P*GP*TP*CP*AP*G)-3') | dna | 5 | — | — |
Ligands and binding sites
- ARS · Arsenic · metal · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
5 interfaces between chains.
- B–A · 342 Ų buried · 33 hydrogen bonds · nucleic-nucleic
- B–C · 333 Ų buried · 36 hydrogen bonds · nucleic-nucleic
- B–D · 264 Ų buried · 29 hydrogen bonds · nucleic-nucleic
- A–C · 102 Ų buried · 3 hydrogen bonds · nucleic-nucleic
- A–D · 101 Ų buried · 3 hydrogen bonds · nucleic-nucleic
Compared structures
- 6UDN · Crystal Structure of a Self-Assembling DNA Scaffold Containing TA Sticky Ends and… · 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 6UDN · PDBe 6UDN
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