Research workbench
G96A mutant of the prpp riboswitch from T. mathranii bound to ppgpp
Analyse G96A mutant of the prpp riboswitch from T. mathranii bound to ppgpp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CK4
- Type
- RNA
- Length
- 414 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prpp riboswitch
- Ligands
- G4P, GTP, K, MG
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prpp riboswitch | rna | 101 | — | — |
| B | Prpp riboswitch | rna | 108 | — | — |
| C | Prpp riboswitch | rna | 106 | — | — |
| D | Prpp riboswitch | rna | 99 | — | — |
Ligands and binding sites
- G4P · Guanosine-5',3'-tetraphosphate · ligand · 4 copies · chains A, B, C, D
- GTP · Guanosine-5'-triphosphate · ligand · chains A
- K · Potassium ion · metal · 27 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 12 copies · chains A, B, C, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 922 | 0.72 | 0.77 | 44 | MG, K, G4P |
| 2 | 664 | 0.66 | 0.77 | 34 | K |
| 3 | 638 | 0.65 | 0.76 | 33 | MG, K |
| 4 | 508 | 0.62 | 0.76 | 26 | empty |
| 5 | 491 | 0.55 | 0.73 | 33 | MG, K, G4P |
Interfaces
4 interfaces between chains.
- A–B · 173 Ų buried · 2 hydrogen bonds · nucleic-nucleic
- B–C · 77 Ų buried · 0 hydrogen bonds · nucleic-nucleic
- B–D · 55 Ų buried · 0 hydrogen bonds · nucleic-nucleic
- A–C · 24 Ų buried · 0 hydrogen bonds · nucleic-nucleic
Compared structures
- 6CK4 · G96A mutant of the PRPP riboswitch from T. mathranii bound to ppGpp · the same entry in another collection · chain D against D, 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 6CK4 · PDBe 6CK4
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