MolNFT v1 · #31667 · DNA
Structural distortions in psoralen cross-linked DNA
2B2B · 5'-D(*CP*CP*GP*CP*TP*AP*GP*CP*GP*G)-3': “Structural distortions in psoralen cross-linked DNA”. X-ray diffraction, 4 ligands (SPM, PSO, NA). MolNFT v1 #31667 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2B2B
- Type
- DNA
- Length
- 20 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*CP*GP*CP*TP*AP*GP*CP*GP*G)-3'
- Ligands
- SPM, PSO, NA, CA
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 5'-D(*CP*CP*GP*CP*TP*AP*GP*CP*GP*G)-3' | dna | 10 | — | — |
Ligands and binding sites
- SPM · Spermine · ligand · chains A
- PSO · 4'-hydroxymethyl-4,5',8-trimethylpsoralen · ligand · chains A, B
- NA · Sodium ion · metal · 3 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
1 interface between chains.
- A–B · 286 Ų buried · 26 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2B2B · Structural distortions in psoralen cross-linked DNA · 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 2B2B · PDBe 2B2B
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