Research workbench
Structure of chicken LGP2 witha 5'P 10-mer dsrna and ADP-ALF4-mg.
Analyse Structure of chicken LGP2 witha 5'P 10-mer dsrna and ADP-ALF4-mg. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JAJ
- Type
- protein + RNA
- Length
- 674 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*CP*GP*UP*AP*CP*CP*C)-3'); RNA…
- UniProt
- G0YYQ5
- Ligands
- ADP, ALF, MGF, ZN, MG
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LGP2 | protein | 653 | 47% helix, 18% strand | G0YYQ5 |
| X | RNA (5'-R(P*GP*GP*UP*AP*CP*GP*UP*AP*CP*CP*C)-3') | rna | 11 | — | — |
| Y | RNA (5'-R(P*GP*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
- MGF · Trifluoromagnesate · ligand · chains A, X, Y
- ZN · Zinc ion · metal · chains A
- MG · Magnesium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · 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 | 1068 | 0.86 | 0.87 | 111 | MGF |
| 2 | 928 | 0.81 | 0.84 | 61 | empty |
| 3 | 205 | 0.67 | 0.86 | 26 | empty |
| 4 | 133 | 0.56 | 0.83 | 28 | ADP, ALF, MG, EDO |
| 5 | 109 | 0.47 | 0.80 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–Y · 1260 Ų buried · 41 hydrogen bonds · protein-nucleic
- A–X · 1184 Ų buried · 24 hydrogen bonds · protein-nucleic
- X–Y · 491 Ų buried · 41 hydrogen bonds · nucleic-nucleic
Compared structures
- 5JAJ · Structure of chicken LGP2 witha 5'p 10-mer dsRNA and ADP-AlF4-Mg. · 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 5JAJ · PDBe 5JAJ · UniProt G0YYQ5
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