Research workbench
T. tengcongensis glms ribozyme with G40A mutation, bound to glucosamine-6-phosphate and a substrate RNA with a 2'5'- phosphodiester linkage
Analyse T. tengcongensis glms ribozyme with G40A mutation, bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3B4B
- Type
- RNA
- Length
- 143 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glms ribozyme substrate with 2'5'-phosphodiester linkage; Glms ribozyme RNA
- Ligands
- GLP, 3AD, MG
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glms ribozyme substrate with 2'5'-phosphodiester linkage | rna | 20 | — | — |
| B | Glms ribozyme RNA | rna | 123 | — | — |
Ligands and binding sites
- GLP · 2-amino-2-deoxy-6-O-phosphono-alpha-D-glucopyranose · ligand · chains A, B
- 3AD · 3'-deoxyadenosine · ligand · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 318 | 0.66 | 0.82 | 29 | GLP, MG |
| 2 | 278 | 0.65 | 0.83 | 20 | empty |
| 3 | 272 | 0.61 | 0.81 | 20 | empty |
| 4 | 431 | 0.55 | 0.74 | 27 | empty |
| 5 | 180 | 0.50 | 0.79 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1427 Ų buried · 110 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3B4B · T. tengcongensis glmS ribozyme with G40A mutation, bound to glucosamine-6-phosphate and a… · 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 3B4B · PDBe 3B4B
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