MolNFT v1 · #66844 · RNA
Crystal structure of the haiprin ribozyme with a 2',5'- linked substrate and N1-deazaadenosine at position A10
3I2U · 5'-R(*UP*CP*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*GP*U)- 3': “Crystal structure of the haiprin ribozyme with a 2',5'- linked substrate and N1-deazaadenosine at position A10”. X-ray diffraction, 3 ligands (NCO, S9L, SO4), 3 pockets (best…
- PDB
- 3I2U
- Type
- RNA
- Length
- 61 nucleotides
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*UP*CP*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*GP*U)- 3'; DNA/RNA (30-mer); 5'…
- Ligands
- NCO, S9L, SO4
- Pockets
- 3 · best druggability 0.42
Structure
x-ray diffraction · 3 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-R(*UP*CP*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*GP*U)- 3' | rna | 13 | — | — |
| B | DNA/RNA (30-mer) | rna | 29 | — | — |
| C | 5'- R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C) -3' | rna | 19 | — | — |
Ligands and binding sites
- NCO · Cobalt hexammine(iii) · ligand · 2 copies · chains B, C, A
- S9L · 2-[2-(2-hydroxyethoxy)ethoxy]ethyl dihydrogen phosphate · ligand · chains B, C
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 199 | 0.42 | 0.74 | 16 | empty |
| 2 | 157 | 0.40 | 0.74 | 17 | empty |
| 3 | 174 | 0.39 | 0.73 | 17 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1015 Ų buried · 74 hydrogen bonds · nucleic-nucleic
- A–B · 799 Ų buried · 46 hydrogen bonds · nucleic-nucleic
- A–C · 343 Ų buried · 7 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 covalent, 1 modified (covalent ligand, nucleotide modification).
Compared structures
- 3I2U · Crystal structure of the haiprin ribozyme with a 2',5'-linked substrate and… · 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 3I2U · PDBe 3I2U
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