MolNFT v1 · #3841 · RNA
29-mer fragment of human srp RNA helix 6
1D4R · 29-mer of modified srp RNA helix 6: “29-mer fragment of human srp RNA helix 6”. X-ray diffraction, 1 ligand (MG), 1 pocket (best druggability 0.60). MolNFT v1 #3841 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1D4R
- Type
- RNA
- Length
- 85 nucleotides
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 29-mer of modified srp RNA helix 6
- Ligands
- MG
- Pockets
- 1 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 29-mer of modified srp RNA helix 6 | rna | 29 | — | — |
| B, C | 29-mer of modified srp RNA helix 6 | rna | 28 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 565 | 0.60 | 0.75 | 31 | MG |
Interfaces
2 interfaces between chains.
- A–B · 1326 Ų buried · 148 hydrogen bonds · nucleic-nucleic
- B–C · 88 Ų buried · 1 hydrogen bond · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 1D4R · 29-mer fragment of human srp rna helix 6 · 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 1D4R · PDBe 1D4R
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