MolNFT v1 · #65283 · DNA
A bulky rhodium complex bound to an adenosine-adenosine DNA mismatch
3GSK · 5'-D(*CP*GP*GP*AP*AP*AP*TP*TP*AP*CP*CP*G)-3': “A bulky rhodium complex bound to an adenosine-adenosine DNA mismatch”. X-ray diffraction, 1 ligand (R1C), 2 pockets (best druggability 0.32). MolNFT v1 #65283 on GenesisL1: 3D…
- PDB
- 3GSK
- Type
- DNA
- Length
- 24 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*GP*GP*AP*AP*AP*TP*TP*AP*CP*CP*G)-3'
- Ligands
- R1C
- Pockets
- 2 · best druggability 0.32
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | 5'-D(*CP*GP*GP*AP*AP*AP*TP*TP*AP*CP*CP*G)-3' | dna | 12 | — | — |
Ligands and binding sites
- R1C · bis(2,2'-bipyridine-kappa~2~N~1~,N~1'~)[chrysene-5,6-diiminato(2-)-kappa~2~N,N']rhodium(4+) · ligand · 2 copies · chains B, A
- CAC · Cacodylate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 94 | 0.32 | 0.73 | 9 | R1C |
| 2 | 77 | 0.30 | 0.74 | 6 | R1C |
Interfaces
1 interface between chains.
- B–A · 581 Ų buried · 42 hydrogen bonds · nucleic-nucleic
Compared structures
- 3GSK · A Bulky Rhodium Complex Bound to an Adenosine-Adenosine DNA Mismatch · 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 3GSK · PDBe 3GSK
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