MolNFT v1 · #108606 · protein + RNA
Crystal structure of tRNA nucleotidyltransferase complexed with a primer tRNA and an incoming ATP analog
4WC2 · Poly a polymerase: “Crystal structure of tRNA nucleotidyltransferase complexed with a primer tRNA and an incoming ATP analog”. X-ray diffraction, 2 ligands (APC, MG), 9 pockets (best druggability 0.74). MolNFT v1 #108606 on…
- PDB
- 4WC2
- Type
- protein + RNA
- Length
- 442 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Poly a polymerase; RNA 75-mer
- UniProt
- O66728
- Ligands
- APC, MG
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Poly a polymerase | protein | 367 | 58% helix, 11% strand | O66728 |
| B | RNA 75-mer | rna | 75 | — | — |
Ligands and binding sites
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · chains A, B
- MG · Magnesium ion · metal
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 862 | 0.74 | 0.79 | 51 | APC, MG |
| 2 | 936 | 0.71 | 0.77 | 42 | empty |
| 3 | 716 | 0.71 | 0.78 | 48 | empty |
| 4 | 383 | 0.57 | 0.76 | 21 | empty |
| 5 | 117 | 0.42 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1083 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 4WC2 · Crystal structure of tRNA nucleotidyltransferase complexed with a primer tRNA and an… · the same entry in another collection · chain A against A, 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 0.99
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 4WC2 · PDBe 4WC2 · UniProt O66728
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