MolNFT v1 · #1 · DNA
100D: Crystal structure of the highly distorted chimeric decamer R(C)D(CGGCGCCG)R(G)-spermine complex-spermine binding to phosphate only and minor groove tertiary base-pairing
100D · DNA/RNA (5'-R(*CP*)-D(*CP*GP*GP*CP*GP*CP*CP*GP*)- R(*G)-3'): “Crystal structure of the highly distorted chimeric decamer R(C)D(CGGCGCCG)R(G)-spermine complex-spermine…”. X-ray diffraction, 1 ligand (SPM), 1 pocket (best druggability…
- PDB
- 100D
- Type
- DNA
- Length
- 20 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Deposited
- 05-DEC-94
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA/RNA (5'-R(*CP*)-D(*CP*GP*GP*CP*GP*CP*CP*GP*)- R(*G)-3')
- Ligands
- SPM
- Pockets
- 1 · best druggability 0.35
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA/RNA (5'-R(*CP*)-D(*CP*GP*GP*CP*GP*CP*CP*GP*)- R(*G)-3') | dna | 10 | — | — |
Ligands and binding sites
- SPM · Spermine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 123 | 0.35 | 0.73 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 540 Ų buried · 53 hydrogen bonds · nucleic-nucleic
Compared structures
- 100D · Crystal structure of the highly distorted chimeric decamer R(C)D(CGGCGCCG)R(G)-spermine… · the same entry in another collection · chain A against A, TM-score 1.00
- 100D · Crystal structure of the highly distorted chimeric decamer R(C)D(CGGCGCCG)R(G)-spermine… · 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 100D · PDBe 100D
Other records of 100D
- 100D · MolNFT v2 / PDB Bank · Crystal structure of the highly distorted chimeric decamer R(C)D(CGGCGCCG)R(G)-spermine…
- 100D-3 · MolNFT · Crystal structure of the highly distorted chimeric decamer R(C)D(CGGCGCCG)R(G)-spermine…
- 100D-4 · MolNFT · Crystal structure of the highly distorted chimeric decamer R(C)D(CGGCGCCG)R(G)-spermine…
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