Research workbench
Structural comparison between the D(CTAG) sequence in oligonucleotides and TRP and met repressor-operator complexes
Analyse Structural comparison between the D(CTAG) sequence in oligonucleotides and TRP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 249D
- Type
- DNA
- Length
- 47 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*CP*GP*CP*TP*CP*TP*AP*GP*AP*GP*CP*G)-3')
- Ligands
- CA
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | DNA (5'-D(*CP*GP*CP*TP*CP*TP*AP*GP*AP*GP*CP*G)-3') | dna | 12 | — | — |
| C | DNA (5'-D(*CP*GP*CP*TP*CP*TP*AP*GP*AP*GP*CP*G)-3') | dna | 11 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
5 interfaces between chains.
- A–B · 553 Ų buried · 64 hydrogen bonds · nucleic-nucleic
- C–D · 544 Ų buried · 60 hydrogen bonds · nucleic-nucleic
- B–D · 86 Ų buried · 0 hydrogen bonds · nucleic-nucleic
- A–D · 34 Ų buried · 1 hydrogen bond · nucleic-nucleic
- B–C · 34 Ų buried · 1 hydrogen bond · nucleic-nucleic
Compared structures
- 249D · Structural comparison between the D(CTAG) sequence in oligonucleotides and TRP and met… · 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 249D · PDBe 249D
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