Research workbench
Crystal structures of CY5 cyanine fluorophores stacked onto the end of double-stranded RNA
Analyse Crystal structures of CY5 cyanine fluorophores stacked onto the end of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NS3
- Type
- protein + RNA
- Length
- 336 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 50S ribosomal protein L5; Double-stranded RNA
- UniProt
- P41201
- Ligands
- 5CY
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 50S ribosomal protein L5 | protein | 135 | 43% helix, 24% strand | P41201 |
| B | 50S ribosomal protein L5 | protein | 138 | 45% helix, 22% strand | P41201 |
| C | Double-stranded RNA | rna | 32 | — | — |
| D | Double-stranded RNA | rna | 31 | — | — |
Ligands and binding sites
- 5CY · 1-(3-hydroxypropyl)-2-{(1E,3E,5E)-5-[1-(3-hydroxypropyl)-3,3-dimethyl-1,3-dihydro-2H-indol-2-ylidene]penta-1,3-dien-1-yl}-3,3-dimethyl-3H-indolium · ligand · 2 copies · chains C, D
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 | 708 | 0.77 | 0.83 | 67 | empty |
| 2 | 516 | 0.74 | 0.83 | 49 | empty |
| 3 | 83 | 0.34 | 0.76 | 12 | empty |
| 4 | 50 | 0.27 | 0.73 | 13 | empty |
| 5 | 58 | 0.27 | 0.73 | 12 | empty |
Interfaces
6 interfaces between chains.
- B–D · 803 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–C · 645 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–D · 474 Ų buried · 18 hydrogen bonds · protein-nucleic
- B–C · 472 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–B · 402 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5NS3 · Crystal structures of Cy5 cyanine fluorophores stacked onto the end of double-stranded RNA · the same entry in another collection · chain A against A, TM-score 1.00
- P41201 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L5 (P41201) · a predicted model of the same protein · chain A 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 P41201
- Elsewhere: RCSB PDB 5NS3 · PDBe 5NS3 · UniProt P41201
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