Research workbench
Crystal structures of an archaeal class I cca-adding enzyme and its nucleotide complexes
Analyse Crystal structures of an archaeal class I cca-adding enzyme and its nucleotide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1R89
- 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
- CTP, MN, NA, MG, CL
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA nucleotidyltransferase (EC 2.7.7.25) | protein | 437 | 45% helix, 22% strand | O28126 |
Ligands and binding sites
- CTP · Cytidine-5'-triphosphate · ligand · 2 copies · chains A
- MN · Manganese (II) ion · metal · 3 copies · chains A
- NA · Sodium ion · metal · chains A
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 647 | 0.70 | 0.78 | 43 | MN, CL, MG, CTP |
| 2 | 55 | 0.58 | 0.90 | 14 | empty |
| 3 | 379 | 0.54 | 0.73 | 25 | empty |
| 4 | 55 | 0.28 | 0.74 | 13 | empty |
Compared structures
- 1R89 · Crystal Structures of an Archaeal Class I CCA-Adding Enzyme and Its Nucleotide Complexes · 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 0.98
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 1R89 · PDBe 1R89 · UniProt O28126
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