Research workbench
Crystal structure of E. COLI tRNA N6-threonylcarbamoyladenosine dehydratase, tcda
Analyse Crystal structure of E. COLI tRNA N6-threonylcarbamoyladenosine dehydratase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RDH
- Type
- protein
- Length
- 971 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA threonylcarbamoyladenosine dehydratase
- EC
- 6.1.-.-
- UniProt
- Q46927
- Ligands
- AMP, SO4
- Pockets
- 13 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA threonylcarbamoyladenosine dehydratase (EC 6.1.-.-) | protein | 245 | 47% helix, 14% strand | Q46927 |
| B, C | TRNA threonylcarbamoyladenosine dehydratase (EC 6.1.-.-) | protein | 243 | 47% helix, 14% strand | Q46927 |
| D | TRNA threonylcarbamoyladenosine dehydratase (EC 6.1.-.-) | protein | 240 | 48% helix, 15% strand | Q46927 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · chains C
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1013 | 0.75 | 0.77 | 82 | empty |
| 2 | 340 | 0.63 | 0.79 | 48 | AMP |
| 3 | 339 | 0.63 | 0.79 | 41 | AMP |
| 4 | 354 | 0.63 | 0.79 | 50 | AMP |
| 5 | 304 | 0.61 | 0.79 | 43 | AMP |
Interfaces
5 interfaces between chains.
- A–B · 2305 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 2136 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 171 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 130 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 63 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 4RDH · Crystal structure of E. coli tRNA N6-threonylcarbamoyladenosine dehydratase, TcdA · the same entry in another collection · chain A against A, TM-score 1.00
- Q46927 · AlphaFold monomer V2.0 prediction for tRNA threonylcarbamoyladenosine dehydratase (Q46927) · a predicted model of the same protein · chain B against A, TM-score 1.00
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 Q46927
- Elsewhere: RCSB PDB 4RDH · PDBe 4RDH · UniProt Q46927
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