Research workbench
Crystal lattice packing is important in determining the bend of a DNA dodecamer containing an adenine tract
Analyse Crystal lattice packing is important in determining the bend of a DNA dodecamer… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1BDN
- Type
- DNA
- Length
- 48 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*CP*GP*CP*AP*AP*AP*AP*AP*TP*GP*CP*G)- 3'); DNA…
- Ligands
- MG
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | DNA (5'-D(*CP*GP*CP*AP*AP*AP*AP*AP*TP*GP*CP*G)- 3') | dna | 12 | — | — |
| B, D | DNA (5'-D(*CP*GP*CP*AP*TP*TP*TP*TP*TP*GP*CP*G)- 3') | dna | 12 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
6 interfaces between chains.
- B–C · 1355 Ų buried · 467 hydrogen bonds · nucleic-nucleic
- A–D · 1344 Ų buried · 462 hydrogen bonds · nucleic-nucleic
- A–C · 602 Ų buried · 84 hydrogen bonds · nucleic-nucleic
- C–D · 592 Ų buried · 66 hydrogen bonds · nucleic-nucleic
- B–D · 570 Ų buried · 26 hydrogen bonds · nucleic-nucleic
Compared structures
- 1BDN · Crystal lattice packing is important in determining the bend of a DNA dodecamer… · 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 1BDN · PDBe 1BDN
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