Research workbench
A cytidine deaminase edits C-to-U in transfer RNAs in archaea
Analyse A cytidine deaminase edits C-to-U in transfer RNAs in archaea in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3G8Q
- Type
- protein
- Length
- 1,109 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.4
- Source
- Methanopyrus kandleri
- Molecule
- Predicted RNA-binding protein, contains THUMP domain
- UniProt
- Q8TWU6
- Ligands
- NA, ZN
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · resolution 2.4 · 2 distinct chains · 31% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Predicted RNA-binding protein, contains THUMP domain | protein | 278 | 31% helix, 32% strand | Q8TWU6 |
| B, C, D | Predicted RNA-binding protein, contains THUMP domain | protein | 277 | 31% helix, 31% strand | Q8TWU6 |
Ligands and binding sites
- NA · Sodium ion · metal · 7 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 995 | 0.77 | 0.79 | 110 | empty |
| 2 | 214 | 0.71 | 0.88 | 29 | empty |
| 3 | 275 | 0.68 | 0.83 | 36 | empty |
| 4 | 65 | 0.64 | 0.93 | 23 | empty |
| 5 | 199 | 0.51 | 0.77 | 28 | ZN |
Interfaces
4 interfaces between chains.
- B–C · 1896 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 1893 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 574 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 64 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3G8Q · A cytidine deaminase edits C-to-U in transfer rnas in archaea · the same entry in another collection · chain D against D, TM-score 1.00
- Q8TWU6 · AlphaFold monomer V2.0 prediction for TRNA(CYTOSINE(8)) deaminase (Q8TWU6) · a predicted model of the same protein · chain D against A, TM-score 0.60
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 Q8TWU6
- Elsewhere: RCSB PDB 3G8Q · PDBe 3G8Q · UniProt Q8TWU6
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