Research workbench
How cca is added to the 3' end of immature tRNA without the use of an oligonucleotide template
Analyse How cca is added to the 3' end of immature tRNA without the use of an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TFW
- Type
- protein + RNA
- Length
- 1,824 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*GP*CP*GP*GP*AP*UP*CP*CP*GP*CP*AP*C)-3'; 5'-R(*GP*CP*GP*GP*AP*UP*CP*CP*GP*CP*AP*CP*C)…
- EC
- 2.7.7.25
- UniProt
- O28126
- Ligands
- ATP, MG
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | 5'-R(*GP*CP*GP*GP*AP*UP*CP*CP*GP*CP*AP*C)-3' | rna | 12 | — | — |
| H, I, G | 5'-R(*GP*CP*GP*GP*AP*UP*CP*CP*GP*CP*AP*CP*C)-3' | rna | 13 | — | — |
| F | 5'-R(*GP*CP*GP*GP*AP*CP*CP*CP*GP*CP*AP*C)-3' | rna | 12 | — | — |
| J | 5'-R(*CP*GP*CP*GP*GP*AP*UP*CP*CP*GP*CP*AP*C)-3' | rna | 13 | — | — |
| A, B, C, D | TRNA nucleotidyltransferase (EC 2.7.7.25) | protein | 437 | 43% helix, 22% strand | O28126 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains H, B, I, D
- MG · Magnesium ion · metal · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1101 | 0.79 | 0.81 | 69 | empty |
| 2 | 548 | 0.77 | 0.84 | 44 | empty |
| 3 | 713 | 0.75 | 0.81 | 65 | MG, ATP |
| 4 | 675 | 0.75 | 0.81 | 59 | MG, ATP |
| 5 | 1151 | 0.72 | 0.75 | 75 | empty |
Interfaces
16 interfaces between chains.
- C–D · 2604 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 2581 Ų buried · 45 hydrogen bonds · protein-protein
- A–C · 1153 Ų buried · 13 hydrogen bonds · protein-protein
- I–D · 889 Ų buried · 28 hydrogen bonds · protein-nucleic
- H–B · 879 Ų buried · 29 hydrogen bonds · protein-nucleic
Compared structures
- 1TFW · How CCA is added to the 3' end of immature tRNA without the use of an oligonucleotide… · the same entry in another collection · chain D against D, TM-score 1.00
- O28126 · AlphaFold monomer V2.0 prediction for cca-adding enzyme (O28126) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 O28126
- Elsewhere: RCSB PDB 1TFW · PDBe 1TFW · UniProt O28126
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