Research workbench
How the cca-adding enzyme selects adenine over cytosine in position 76 of tRNA
Analyse How the cca-adding enzyme selects adenine over cytosine in position 76 of tRNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OVA
- Type
- protein + RNA
- Length
- 464 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cca-adding enzyme; RNA (34-mer)
- EC
- 2.7.7.25, 2.7.7.21
- UniProt
- O28126
- Ligands
- APC, MG, SO4
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cca-adding enzyme (EC 2.7.7.25, 2.7.7.21) | protein | 430 | 45% helix, 22% strand | O28126 |
| C | RNA (34-mer) | rna | 34 | — | — |
Ligands and binding sites
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · chains A, C
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A, C
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 575 | 0.74 | 0.82 | 48 | APC, MG |
| 2 | 515 | 0.58 | 0.73 | 46 | empty |
| 3 | 462 | 0.55 | 0.73 | 30 | SO4 |
| 4 | 366 | 0.53 | 0.73 | 27 | empty |
| 5 | 151 | 0.44 | 0.76 | 26 | EDO |
Interfaces
1 interface between chains.
- A–C · 1489 Ų buried · 44 hydrogen bonds · protein-nucleic
Compared structures
- 3OVA · How the CCA-adding Enzyme Selects Adenine over Cytosine in Position 76 of tRNA · the same entry in another collection · chain A against A, TM-score 1.00
- O28126 · AlphaFold monomer V2.0 prediction for cca-adding enzyme (O28126) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 3OVA · PDBe 3OVA · UniProt O28126
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