MolNFT v1 · #20233 · protein
Crystal structures of an archaeal class I cca-adding enzyme and its nucleotide
1R8C · TRNA nucleotidyltransferase: “Crystal structures of an archaeal class I cca-adding enzyme and its nucleotide”. X-ray diffraction, 3 ligands (UTP, MN, NA), 5 pockets (best druggability 0.71). MolNFT v1 #20233 on GenesisL1: 3D…
- PDB
- 1R8C
- Type
- protein
- Length
- 437 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA nucleotidyltransferase
- EC
- 2.7.7.25
- UniProt
- O28126
- Ligands
- UTP, MN, NA
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA nucleotidyltransferase (EC 2.7.7.25) | protein | 437 | 44% helix, 22% strand | O28126 |
Ligands and binding sites
- UTP · Uridine 5'-triphosphate · ligand · 2 copies · chains A
- MN · Manganese (II) ion · metal · 5 copies · chains A
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 670 | 0.71 | 0.78 | 46 | MN, UTP |
| 2 | 387 | 0.54 | 0.73 | 29 | empty |
| 3 | 68 | 0.53 | 0.86 | 14 | empty |
| 4 | 55 | 0.31 | 0.76 | 13 | empty |
| 5 | 51 | 0.28 | 0.74 | 12 | empty |
Compared structures
- 1R8C · Crystal Structures of an Archaeal Class I CCA-Adding Enzyme and Its Nucleotide · 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 1R8C · PDBe 1R8C · UniProt O28126
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