Research workbench
Crystal structure of rtca, the RNA 3'-terminal phosphate cyclase from pyrococcus horikoshii.
Analyse Crystal structure of rtca, the RNA 3'-terminal phosphate cyclase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4O89
- Type
- protein
- Length
- 682 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA 3'-terminal phosphate cyclase
- EC
- 6.5.1.4
- UniProt
- O59198
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RNA 3'-terminal phosphate cyclase (EC 6.5.1.4) | protein | 341 | 33% helix, 30% strand | O59198 |
Ligands and binding sites
- CIT · Citric acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 362 | 0.79 | 0.89 | 49 | CIT |
| 2 | 830 | 0.74 | 0.78 | 83 | empty |
| 3 | 179 | 0.55 | 0.80 | 28 | empty |
| 4 | 304 | 0.54 | 0.75 | 38 | CIT |
Interfaces
1 interface between chains.
- A–B · 872 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4O89 · Crystal structure of RtcA, the RNA 3'-terminal phosphate cyclase from Pyrococcus… · the same entry in another collection · chain A against A, TM-score 1.00
- O59198 · AlphaFold monomer V2.0 prediction for RNA 3'-terminal phosphate cyclase (O59198) · 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 O59198
- Elsewhere: RCSB PDB 4O89 · PDBe 4O89 · UniProt O59198
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