MolNFT v1 · #125133 · RNA
Self-complimentary RNA 15MER binding with gmp monomers
5L00 · RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)…: “Self-complimentary RNA 15MER binding with gmp monomers”. X-ray diffraction, 2 ligands (G, MG), 2 pockets (best druggability 0.44). MolNFT v1 #125133 on GenesisL1: 3D structure, binding sites…
- PDB
- 5L00
- Type
- RNA
- Length
- 60 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG) P*AP*CP*UP*UP*AP*AP*GP*UP*CP*GP*G)-3')
- Ligands
- G, MG
- Pockets
- 2 · best druggability 0.44
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG) P*AP*CP*UP*UP*AP*AP*GP*UP*CP*GP*G)-3') | rna | 15 | — | — |
Ligands and binding sites
- G · Guanosine-5'-monophosphate · ligand · 4 copies · chains A, B, D, C
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
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 | 239 | 0.44 | 0.73 | 20 | empty |
| 2 | 219 | 0.42 | 0.72 | 17 | empty |
Interfaces
3 interfaces between chains.
- C–D · 691 Ų buried · 57 hydrogen bonds · nucleic-nucleic
- A–B · 689 Ų buried · 56 hydrogen bonds · nucleic-nucleic
- B–D · 74 Ų buried · 1 hydrogen bond · nucleic-nucleic
Modifications
Observed in the structure: 16 modified (nucleotide modification).
Compared structures
- 5L00 · Self-complimentary RNA 15mer binding with GMP monomers · 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 5L00 · PDBe 5L00
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