MolNFT v1 · #123161 · protein + RNA
Crystal structure of chicken LGP2 with 5'PPP 26-mer hairpin RNA with 3' gg overhang and ADP-ALF4-MG2+ at 2.0 a resolution.
5JBG: “Crystal structure of chicken LGP2 with 5'PPP 26-mer hairpin RNA with 3' gg overhang and ADP-ALF4-MG2+ at 2.0…”. X-ray diffraction, 5 ligands (ADP, ALF, ZN), 9 pockets (best druggability 0.87). MolNFT v1 #123161 on GenesisL1: 3D…
- PDB
- 5JBG
- Type
- protein + RNA
- Length
- 684 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LGP2; RNA (5'- R(*GPPP*GP*AP*GP*CP*GP*UP*GP*CP*CP*GP*GP*GP*CP*AP*CP*GP*CP*UP*CP*CP*G…
- UniProt
- G0YYQ5
- Ligands
- ADP, ALF, ZN, MG, SO4
- Pockets
- 9 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LGP2 | protein | 661 | 47% helix, 18% strand | G0YYQ5 |
| X | RNA (5'- R(*GPPP*GP*AP*GP*CP*GP*UP*GP*CP*CP*GP*GP*GP*CP*AP*CP*GP*CP*UP*CP*CP*G P*G)-3') | rna | 23 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- ALF · Tetrafluoroaluminate ion · ligand · chains A
- ZN · Zinc ion · metal · chains A
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A, X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1159 | 0.87 | 0.89 | 103 | SO4 |
| 2 | 197 | 0.69 | 0.87 | 31 | empty |
| 3 | 363 | 0.67 | 0.81 | 38 | empty |
| 4 | 361 | 0.66 | 0.80 | 43 | ADP, ALF, MG |
| 5 | 100 | 0.47 | 0.80 | 20 | empty |
Interfaces
1 interface between chains.
- A–X · 2818 Ų buried · 59 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 5JBG · Crystal structure of chicken LGP2 with 5'ppp 26-mer hairpin RNA with 3' GG overhang and… · the same entry in another collection · chain A against A, TM-score 1.00
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 G0YYQ5
- Elsewhere: RCSB PDB 5JBG · PDBe 5JBG · UniProt G0YYQ5
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