MolNFT v1 · #58457 · RNA
T. tengcongensis glms ribozyme with G40A mutation, bound to glucosamine-6-phosphate
3B4A · Glms ribozyme substrate RNA: “T. tengcongensis glms ribozyme with G40A mutation, bound to glucosamine-6-phosphate”. X-ray diffraction, 2 ligands (GLP, MG), 5 pockets (best druggability 0.66). MolNFT v1 #58457 on GenesisL1: 3D…
- PDB
- 3B4A
- Type
- RNA
- Length
- 144 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glms ribozyme substrate RNA; Glms ribozyme RNA
- Ligands
- GLP, MG
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glms ribozyme substrate RNA | rna | 22 | — | — |
| B | Glms ribozyme RNA | rna | 122 | — | — |
Ligands and binding sites
- GLP · 2-amino-2-deoxy-6-O-phosphono-alpha-D-glucopyranose · ligand · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 402 | 0.66 | 0.80 | 35 | empty |
| 2 | 171 | 0.59 | 0.83 | 24 | GLP |
| 3 | 474 | 0.57 | 0.74 | 29 | MG |
| 4 | 348 | 0.52 | 0.74 | 23 | empty |
| 5 | 179 | 0.50 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1527 Ų buried · 89 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3B4A · T. tengcongensis glmS ribozyme with G40A mutation, bound to glucosamine-6-phosphate · 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 3B4A · PDBe 3B4A
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