MolNFT v1 · #88839 · protein
Crystal structure of E. COLI tRNA N6-threonylcarbamoyladenosine dehydratase, tcda, in complex with ATP at 1.768 angstroem resolution
4D79 · TRNA threonylcarbamoyladenosine dehydratase: “Crystal structure of E. COLI tRNA N6-threonylcarbamoyladenosine dehydratase, tcda, in complex with ATP at…”. X-ray diffraction, 3 ligands (ATP, K, NA), 11 pockets (best druggability…
- PDB
- 4D79
- Type
- protein
- Length
- 985 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
- ATP, K, NA
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA threonylcarbamoyladenosine dehydratase (EC 6.1.-.-) | protein | 243 | 47% helix, 14% strand | Q46927 |
| B | TRNA threonylcarbamoyladenosine dehydratase (EC 6.1.-.-) | protein | 247 | 47% helix, 14% strand | Q46927 |
| C | TRNA threonylcarbamoyladenosine dehydratase (EC 6.1.-.-) | protein | 251 | 45% helix, 14% strand | Q46927 |
| D | TRNA threonylcarbamoyladenosine dehydratase (EC 6.1.-.-) | protein | 244 | 47% helix, 15% strand | Q46927 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 2 copies · chains A, B, C, D
- GOL · Glycerol · additive · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 813 | 0.79 | 0.82 | 81 | GOL |
| 2 | 491 | 0.74 | 0.83 | 58 | ATP |
| 3 | 311 | 0.62 | 0.79 | 43 | ATP |
| 4 | 344 | 0.62 | 0.79 | 45 | ATP |
| 5 | 328 | 0.62 | 0.79 | 43 | ATP |
Interfaces
6 interfaces between chains.
- A–B · 2321 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 2235 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 477 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 189 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 175 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4D79 · Crystal structure of E. coli tRNA N6-threonylcarbamoyladenosine dehydratase, TcdA, in… · the same entry in another collection · chain D against D, TM-score 1.00
- Q46927 · AlphaFold monomer V2.0 prediction for tRNA threonylcarbamoyladenosine dehydratase (Q46927) · a predicted model of the same protein · chain A 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 4D79 · PDBe 4D79 · UniProt Q46927
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