MolNFT v1 · #122440 · DNA
Lambda-RU(TAP)2DPPZ bound to D(CCGGCTCCGG)
5IP8 · DNA (5'-D(*CP*CP*GP*GP*AP*GP*CP*CP*GP*G)-3'): “Lambda-RU(TAP)2DPPZ bound to D(CCGGCTCCGG)”. X-ray diffraction, 2 ligands (RKL, BA). MolNFT v1 #122440 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5IP8
- Type
- DNA
- Length
- 20 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*CP*CP*GP*GP*AP*GP*CP*CP*GP*G)-3'); DNA (5'-D(*CP*CP*GP*GP*CP*TP*CP*CP*GP*G)-3')
- Ligands
- RKL, BA
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA (5'-D(*CP*CP*GP*GP*AP*GP*CP*CP*GP*G)-3') | dna | 10 | — | — |
| A | DNA (5'-D(*CP*CP*GP*GP*CP*TP*CP*CP*GP*G)-3') | dna | 10 | — | — |
Ligands and binding sites
- RKL · Ru(tap)2(dppz) complex · ligand · 2 copies · chains B, A
- BA · Barium ion · metal · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
1 interface between chains.
- B–A · 476 Ų buried · 39 hydrogen bonds · nucleic-nucleic
Compared structures
- 5IP8 · Lambda-Ru(TAP)2dppz bound to d(CCGGCTCCGG) · 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 5IP8 · PDBe 5IP8
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