Research workbench
Complex of D(CCTAGG) with tetra-[N-methyl-pyridyl] porphyrin
Analyse Complex of D(CCTAGG) with tetra-[N-methyl-pyridyl] porphyrin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EM0
- Type
- DNA
- Length
- 24 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*(CBR)P*CP*TP*AP*GP*G)-3')
- Ligands
- PNI, MG
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | DNA (5'-D(*(CBR)P*CP*TP*AP*GP*G)-3') | dna | 6 | — | — |
Ligands and binding sites
- PNI · Tetra[n-methyl-pyridyl] porphyrin-nickel · ligand · 2 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
6 interfaces between chains.
- A–B · 283 Ų buried · 19 hydrogen bonds · nucleic-nucleic
- C–D · 280 Ų buried · 19 hydrogen bonds · nucleic-nucleic
- A–D · 112 Ų buried · 3 hydrogen bonds · nucleic-nucleic
- B–C · 111 Ų buried · 3 hydrogen bonds · nucleic-nucleic
- A–C · 36 Ų buried · 0 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 1EM0 · Complex of D(CCTAGG) with tetra-[N-methyl-pyridyl] porphyrin · 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 1EM0 · PDBe 1EM0
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