Research workbench
20A mutant C-di-gmp VC2 riboswitch bound with 3',3'-cgamp
Analyse 20A mutant C-di-gmp VC2 riboswitch bound with 3',3'-cgamp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YB1
- Type
- protein + RNA
- Length
- 183 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (91-mer); U1 small nuclear ribonucleoprotein a
- UniProt
- P09012
- Ligands
- 4BW, MG
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | RNA (91-mer) | rna | 91 | — | — |
| P | U1 small nuclear ribonucleoprotein a | protein | 92 | 32% helix, 28% strand | P09012 |
Ligands and binding sites
- 4BW · 2-amino-9-[(2r,3r,3as,5r,7ar,9r,10r,10as,12r,14ar)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-D:3',2'-J][1,3,7,9, 2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6H-purin-6-one · ligand · chains R
- MG · Magnesium ion · metal · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 501 | 0.64 | 0.77 | 26 | empty |
| 2 | 392 | 0.58 | 0.76 | 25 | MG |
| 3 | 88 | 0.41 | 0.79 | 9 | empty |
| 4 | 74 | 0.38 | 0.79 | 11 | 4BW |
| 5 | 129 | 0.36 | 0.74 | 12 | empty |
Interfaces
1 interface between chains.
- R–P · 164 Ų buried · 1 hydrogen bond · protein-nucleic
Compared structures
- 4YB1 · 20A Mutant c-di-GMP Vc2 Riboswitch bound with 3',3'-cGAMP · the same entry in another collection · chain R against R, 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 P 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 4YB1 · PDBe 4YB1 · UniProt P09012
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