Research workbench
Crystal structure of tRNA nucleotidyltransferase complexed with a primer tRNA and an incoming ATP analog
Analyse Crystal structure of tRNA nucleotidyltransferase complexed with a primer tRNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VFG
- Type
- protein + RNA
- Length
- 765 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (75-mer); Poly a polymerase
- EC
- 2.7.7.19
- UniProt
- O66728
- Ligands
- APC
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 57% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | RNA (75-mer) | rna | 31 | — | — |
| D | RNA (75-mer) | rna | 34 | — | — |
| A | Poly a polymerase (EC 2.7.7.19) | protein | 342 | 56% helix, 11% strand | O66728 |
| B | Poly a polymerase (EC 2.7.7.19) | protein | 358 | 58% helix, 10% strand | O66728 |
Ligands and binding sites
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · 2 copies · chains A, D, B
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 | 658 | 0.73 | 0.80 | 46 | APC |
| 2 | 636 | 0.71 | 0.79 | 34 | empty |
| 3 | 477 | 0.66 | 0.78 | 30 | empty |
| 4 | 633 | 0.64 | 0.75 | 34 | empty |
| 5 | 185 | 0.63 | 0.84 | 27 | empty |
Interfaces
3 interfaces between chains.
- D–B · 874 Ų buried · 19 hydrogen bonds · protein-nucleic
- C–A · 464 Ų buried · 4 hydrogen bonds · protein-nucleic
- A–B · 114 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1VFG · Crystal structure of tRNA nucleotidyltransferase complexed with a primer tRNA and an… · the same entry in another collection · chain C against C, TM-score 1.00
- O66728 · AlphaFold monomer V2.0 prediction for a-adding tRNA nucleotidyltransferase (O66728) · 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 O66728
- Elsewhere: RCSB PDB 1VFG · PDBe 1VFG · UniProt O66728
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