MolNFT v1 · #123147 · protein + RNA
Crystal structure of chicken LGP2 with 5'PPP 10-mer dsrna and ADP- ALF4-MG2+ at 2.2 a resolution.
5JB2: “Crystal structure of chicken LGP2 with 5'PPP 10-mer dsrna and ADP- ALF4-MG2+ at 2.2 a resolution.”. X-ray diffraction, 4 ligands (ADP, ALF, MG), 8 pockets (best druggability 0.86). MolNFT v1 #123147 on GenesisL1: 3D structure…
- PDB
- 5JB2
- Type
- protein + RNA
- Length
- 691 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LGP2; RNA (5'-R(*GPPP*GP*UP*AP*CP*GP*UP*AP*CP*CP*C)-3'); RNA…
- UniProt
- G0YYQ5
- Ligands
- ADP, ALF, MG, ZN
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LGP2 | protein | 670 | 46% helix, 17% strand | G0YYQ5 |
| X | RNA (5'-R(*GPPP*GP*UP*AP*CP*GP*UP*AP*CP*CP*C)-3') | rna | 11 | — | — |
| Y | RNA (5'-R(*GPPP*GP*UP*AP*CP*GP*UP*AP*CP*C)-3') | rna | 10 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- ALF · Tetrafluoroaluminate ion · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A, X
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 763 | 0.86 | 0.89 | 85 | empty |
| 2 | 917 | 0.82 | 0.84 | 67 | empty |
| 3 | 554 | 0.70 | 0.79 | 54 | ADP, ALF, MG |
| 4 | 187 | 0.70 | 0.88 | 26 | empty |
| 5 | 201 | 0.69 | 0.87 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–Y · 1243 Ų buried · 36 hydrogen bonds · protein-nucleic
- A–X · 1231 Ų buried · 28 hydrogen bonds · protein-nucleic
- X–Y · 503 Ų buried · 43 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 5JB2 · Crystal structure of chicken LGP2 with 5'ppp 10-mer dsRNA and ADP-AlF4-Mg2+ at 2.2 A… · 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 5JB2 · PDBe 5JB2 · UniProt G0YYQ5
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