MolNFT v1 · #108513 · protein + RNA
Crystal structure of bacillus subtilis cyclic-di-AMP riboswitch ydao
4W92 · U1 small nuclear ribonucleoprotein a: “Crystal structure of bacillus subtilis cyclic-di-AMP riboswitch ydao”. X-ray diffraction, 3 ligands (2BA, MG, K), 4 pockets (best druggability 0.58). MolNFT v1 #108513 on GenesisL1: 3D…
- PDB
- 4W92
- Type
- protein + RNA
- Length
- 185 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- U1 small nuclear ribonucleoprotein a; C-di-AMP ribsoswitch
- UniProt
- P09012
- Ligands
- 2BA, MG, K
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | U1 small nuclear ribonucleoprotein a | protein | 90 | 33% helix, 28% strand | P09012 |
| C | C-di-AMP ribsoswitch | rna | 95 | — | — |
Ligands and binding sites
- 2BA · (2r,3r,3as,5r,7ar,9r,10r,10as,12r,14ar)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-D:3', 2'-J][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5, 10,12-tetrol 5,12-dioxide · ligand · 2 copies · chains C
- MG · Magnesium ion · metal · 5 copies · chains C
- K · Potassium ion · metal · chains C
- EDO · 1,2-ethanediol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 471 | 0.58 | 0.74 | 35 | 2BA |
| 2 | 233 | 0.48 | 0.75 | 30 | MG |
| 3 | 195 | 0.46 | 0.75 | 24 | empty |
| 4 | 112 | 0.33 | 0.73 | 14 | MG, EDO |
Interfaces
1 interface between chains.
- B–C · 708 Ų buried · 22 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 3 modified (engineered).
Compared structures
- 4W92 · Crystal structure of Bacillus subtilis cyclic-di-AMP riboswitch ydaO · the same entry in another collection · chain B against B, 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 B against A, TM-score 0.99
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 4W92 · PDBe 4W92 · UniProt P09012
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