MolNFT v1 · #123164 · protein + RNA
Crystal structure of chicken LGP2 with 5'P 12-mer dsrna at 3.6 a resolution
5JBJ: “Crystal structure of chicken LGP2 with 5'P 12-mer dsrna at 3.6 a resolution”. X-ray diffraction, 1 ligand (ZN), 9 pockets (best druggability 0.83). MolNFT v1 #123164 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5JBJ
- Type
- protein + RNA
- Length
- 651 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LGP2; RNA (5'-R(P*GP*GP*UP*AP*GP*CP*GP*CP*UP*AP*CP*C)-3')
- UniProt
- G0YYQ5
- Ligands
- ZN
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LGP2 | protein | 627 | 45% helix, 16% strand | G0YYQ5 |
| X, Y | RNA (5'-R(P*GP*GP*UP*AP*GP*CP*GP*CP*UP*AP*CP*C)-3') | rna | 12 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
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 | 1164 | 0.83 | 0.84 | 103 | empty |
| 2 | 748 | 0.81 | 0.85 | 43 | empty |
| 3 | 443 | 0.72 | 0.83 | 50 | empty |
| 4 | 244 | 0.71 | 0.87 | 33 | empty |
| 5 | 154 | 0.49 | 0.78 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–Y · 1256 Ų buried · 31 hydrogen bonds · protein-nucleic
- A–X · 1115 Ų buried · 16 hydrogen bonds · protein-nucleic
- X–Y · 572 Ų buried · 55 hydrogen bonds · nucleic-nucleic
Compared structures
- 5JBJ · Crystal structure of chicken LGP2 with 5'p 12-mer dsRNA at 3.6 A resolution · 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 5JBJ · PDBe 5JBJ · UniProt G0YYQ5
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