Research workbench
Co-crystal structure of a bacterial C-di-gmp riboswitch
Analyse Co-crystal structure of a bacterial C-di-gmp riboswitch in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IWN
- Type
- protein + RNA
- Length
- 368 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-di-gmp riboswitch; U1 small nuclear ribonucleoprotein a
- UniProt
- P09012
- Ligands
- C2E
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | C-di-gmp riboswitch | rna | 93 | — | — |
| C, D | U1 small nuclear ribonucleoprotein a | protein | 91 | 27% helix, 26% strand | P09012 |
Ligands and binding sites
- C2E · 9,9'-[(2r,3r,3as,5s,7ar,9r,10r,10as,12s,14ar)-3,5,10, 12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3, 2-D:3',2'-J][1,3,7,9,2, 8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 620 | 0.69 | 0.78 | 42 | empty |
| 2 | 511 | 0.68 | 0.79 | 36 | empty |
| 3 | 757 | 0.66 | 0.75 | 38 | empty |
| 4 | 545 | 0.61 | 0.75 | 40 | empty |
| 5 | 282 | 0.57 | 0.78 | 16 | C2E |
Interfaces
3 interfaces between chains.
- A–C · 918 Ų buried · 31 hydrogen bonds · protein-nucleic
- B–D · 893 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–D · 431 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 3IWN · Co-crystal structure of a bacterial c-di-GMP riboswitch · the same entry in another collection · chain A against A, TM-score 1.00
- P09012 · AlphaFold monomer V2.0 prediction for U1 small nuclear ribonucleoprotein a (P09012) · a predicted model of the same protein · chain D against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P09012
- Elsewhere: RCSB PDB 3IWN · PDBe 3IWN · UniProt P09012
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.