MolNFT v1 · #17721 · DNA
Crystal structure of NICKEL(II)-D(GGCGCC)2
1P25 · 5'-D(*GP*GP*CP*GP*CP*C)-3': “Crystal structure of NICKEL(II)-D(GGCGCC)2”. X-ray diffraction, 1 ligand (NI). MolNFT v1 #17721 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1P25
- Type
- DNA
- Length
- 30 nucleotides
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*GP*CP*GP*CP*C)-3'
- Ligands
- NI
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | 5'-D(*GP*GP*CP*GP*CP*C)-3' | dna | 6 | — | — |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
8 interfaces between chains.
- B–C · 282 Ų buried · 32 hydrogen bonds · nucleic-nucleic
- D–E · 279 Ų buried · 34 hydrogen bonds · nucleic-nucleic
- C–E · 137 Ų buried · 4 hydrogen bonds · nucleic-nucleic
- B–D · 133 Ų buried · 2 hydrogen bonds · nucleic-nucleic
- A–B · 128 Ų buried · 0 hydrogen bonds · nucleic-nucleic
Compared structures
- 1P25 · Crystal structure of nickel(II)-d(GGCGCC)2 · 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 1P25 · PDBe 1P25
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