Research workbench
Crystal structures of CY3 cyanine fluorophores stacked onto the end of double-stranded RNA
Analyse Crystal structures of CY3 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
- 5NS4
- Type
- protein + RNA
- Length
- 346 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 50S ribosomal protein L5; RNA (34-mer)
- UniProt
- P41201
- Ligands
- 96T, MG
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 50S ribosomal protein L5 | protein | 138 | 42% helix, 26% strand | P41201 |
| B | 50S ribosomal protein L5 | protein | 146 | 42% helix, 25% strand | P41201 |
| C | RNA (34-mer) | rna | 32 | — | — |
| D | RNA (34-mer) | rna | 30 | — | — |
Ligands and binding sites
- 96T · 3-[(2~{Z})-2-[(~{E})-3-[3,3-dimethyl-1-(3-oxidanylpropyl)indol-1-ium-2-yl]prop-2-enylidene]-3,3-dimethyl-indol-1-yl]propan-1-ol · ligand · chains C
- MG · Magnesium ion · metal · 7 copies · chains A, B, 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1172 | 0.81 | 0.83 | 97 | MG |
| 2 | 139 | 0.46 | 0.77 | 18 | empty |
| 3 | 140 | 0.45 | 0.76 | 20 | empty |
| 4 | 61 | 0.45 | 0.82 | 11 | empty |
| 5 | 67 | 0.30 | 0.75 | 12 | MG |
Interfaces
6 interfaces between chains.
- B–D · 789 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–C · 717 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–D · 482 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–C · 472 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–B · 373 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5NS4 · Crystal structures of Cy3 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 B 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 5NS4 · PDBe 5NS4 · UniProt P41201
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