MolNFT v1 · #73021 · RNA
Structure of the S-adenosylhomocysteine riboswitch at 2.18 a
3NPQ: “Structure of the S-adenosylhomocysteine riboswitch at 2.18 a”. X-ray diffraction, 2 ligands (NCO, SAH), 6 pockets (best druggability 0.44). MolNFT v1 #73021 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3NPQ
- Type
- RNA
- Length
- 150 nucleotides
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-adenosylhomocysteine riboswitch
- Ligands
- NCO, SAH
- Pockets
- 6 · best druggability 0.44
Structure
x-ray diffraction · 3 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-adenosylhomocysteine riboswitch | rna | 51 | — | — |
| B | S-adenosylhomocysteine riboswitch | rna | 49 | — | — |
| C | S-adenosylhomocysteine riboswitch | rna | 50 | — | — |
Ligands and binding sites
- NCO · Cobalt hexammine(iii) · ligand · 15 copies · chains A, B, C
- SAH · S-adenosyl-L-homocysteine · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 245 | 0.44 | 0.73 | 16 | empty |
| 2 | 234 | 0.44 | 0.73 | 19 | NCO |
| 3 | 226 | 0.43 | 0.73 | 16 | empty |
| 4 | 123 | 0.34 | 0.73 | 15 | NCO |
| 5 | 62 | 0.30 | 0.75 | 10 | SAH |
Interfaces
3 interfaces between chains.
- B–C · 186 Ų buried · 6 hydrogen bonds · nucleic-nucleic
- A–B · 184 Ų buried · 6 hydrogen bonds · nucleic-nucleic
- A–C · 181 Ų buried · 5 hydrogen bonds · nucleic-nucleic
Compared structures
- 3NPQ · Structure of the S-adenosylhomocysteine riboswitch at 2.18 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 3NPQ · PDBe 3NPQ
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