Research workbench
Crystal structure of a group II intron lariat in the post-catalytic state
Analyse Crystal structure of a group II intron lariat in the post-catalytic state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CIH
- Type
- RNA
- Length
- 630 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (696-mer); RNA (5'-R(P*UP*GP*UP*UP*UP*AP*UP*UP*AP*AP*AP*AP*AP*C*-3')
- Ligands
- IRI, MG, NA
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA (696-mer) | rna | 616 | — | — |
| B | RNA (5'-R(P*UP*GP*UP*UP*UP*AP*UP*UP*AP*AP*AP*AP*AP*C*-3') | rna | 14 | — | — |
Ligands and binding sites
- IRI · Iridium hexammine ion · ligand · 41 copies · chains A
- MG · Magnesium ion · metal · 86 copies · chains A, B
- NA · Sodium ion · metal · 9 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 804 | 0.73 | 0.79 | 57 | IRI, MG |
| 2 | 935 | 0.71 | 0.77 | 57 | IRI, MG |
| 3 | 407 | 0.71 | 0.83 | 34 | NA, MG |
| 4 | 1015 | 0.69 | 0.75 | 42 | IRI, MG |
| 5 | 765 | 0.67 | 0.76 | 38 | IRI, MG |
Interfaces
1 interface between chains.
- A–B · 1127 Ų buried · 52 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6CIH · Crystal structure of a group II intron lariat in the post-catalytic state · 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
- Elsewhere: RCSB PDB 6CIH · PDBe 6CIH
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