MolNFT v1 · #145225 · RNA
Crystal structure of a group II intron lariat with an intact 3' splice site (pre-2S state)
6CHR · RNA (621-mer): “Crystal structure of a group II intron lariat with an intact 3' splice site (pre-2S state)”. X-ray diffraction, 3 ligands (SPM, MG, NA), 20 pockets (best druggability 0.73). MolNFT v1 #145225 on GenesisL1: 3D…
- PDB
- 6CHR
- Type
- RNA
- Length
- 633 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (621-mer); RNA (5'-R(P*UP*GP*UP*UP*UP*AP*UP*UP*AP*AP*AP*AP*A)-3')
- Ligands
- SPM, MG, NA
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA (621-mer) | rna | 620 | — | — |
| B | RNA (5'-R(P*UP*GP*UP*UP*UP*AP*UP*UP*AP*AP*AP*AP*A)-3') | rna | 13 | — | — |
Ligands and binding sites
- SPM · Spermine · ligand · chains A
- MG · Magnesium ion · metal · 82 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 548 | 0.73 | 0.82 | 47 | MG |
| 2 | 728 | 0.73 | 0.80 | 53 | NA, MG |
| 3 | 484 | 0.70 | 0.81 | 51 | MG |
| 4 | 476 | 0.68 | 0.80 | 35 | MG |
| 5 | 521 | 0.67 | 0.79 | 42 | empty |
Interfaces
1 interface between chains.
- A–B · 1109 Ų buried · 47 hydrogen bonds · nucleic-nucleic
Compared structures
- 6CHR · Crystal structure of a group II intron lariat with an intact 3' splice site (pre-2s 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 6CHR · PDBe 6CHR
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