Research workbench
Class II ligase ribozyme product-template duplex, structure 1
Analyse Class II ligase ribozyme product-template duplex, structure 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FTM
- Type
- RNA
- Length
- 46 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*GP*UP*GP*UP*GP*AP*GP*GP*CP*UP*G)-3'; 5'-R(*CP*CP*AP*GP*UP*CP*GP*GP*AP*AP*CP*A)-3'
- Ligands
- MG, K
- Pockets
- 2 · best druggability 0.26
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 5'-R(*GP*UP*GP*UP*GP*AP*GP*GP*CP*UP*G)-3' | rna | 11 | — | — |
| B, D | 5'-R(*CP*CP*AP*GP*UP*CP*GP*GP*AP*AP*CP*A)-3' | rna | 12 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 9 copies · chains A, B, D, C
- K · Potassium ion · metal · 2 copies · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.26 | 0.73 | 9 | MG |
| 2 | 50 | 0.21 | 0.72 | 12 | empty |
Interfaces
5 interfaces between chains.
- C–D · 623 Ų buried · 53 hydrogen bonds · nucleic-nucleic
- A–B · 606 Ų buried · 54 hydrogen bonds · nucleic-nucleic
- B–C · 145 Ų buried · 8 hydrogen bonds · nucleic-nucleic
- B–D · 115 Ų buried · 3 hydrogen bonds · nucleic-nucleic
- A–D · 72 Ų buried · 1 hydrogen bond · nucleic-nucleic
Compared structures
- 3FTM · Class II ligase ribozyme product-template duplex, structure 1 · 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 3FTM · PDBe 3FTM
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