MolNFT v1 · #109038 · protein
YGJD(V85E)-yeaz heterodimer in complex with ATP
4WQ5 · TRNA N6-adenosine threonylcarbamoyltransferase: “YGJD(V85E)-yeaz heterodimer in complex with ATP”. X-ray diffraction, 3 ligands (ATP, MG, FE), 9 pockets (best druggability 0.75). MolNFT v1 #109038 on GenesisL1: 3D structure, binding…
- PDB
- 4WQ5
- Type
- protein
- Length
- 1,122 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA N6-adenosine threonylcarbamoyltransferase; TRNA threonylcarbamoyladenosine…
- EC
- 2.6.99.4
- UniProt
- P05852, P76256
- Ligands
- ATP, MG, FE
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA N6-adenosine threonylcarbamoyltransferase (EC 2.6.99.4) | protein | 332 | 46% helix, 20% strand | P05852 |
| B | TRNA N6-adenosine threonylcarbamoyltransferase (EC 2.6.99.4) | protein | 336 | 47% helix, 20% strand | P05852 |
| C | TRNA threonylcarbamoyladenosine biosynthesis protein tsab | protein | 226 | 36% helix, 29% strand | P76256 |
| D | TRNA threonylcarbamoyladenosine biosynthesis protein tsab | protein | 228 | 35% helix, 29% strand | P76256 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- FE · Fe (III) ion · metal · 2 copies · chains A, B
- ACT · Acetate ion · additive · 8 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 877 | 0.75 | 0.79 | 100 | MG, FE, ATP, ACT |
| 2 | 581 | 0.68 | 0.77 | 51 | MG, FE, ATP |
| 3 | 528 | 0.67 | 0.77 | 51 | empty |
| 4 | 157 | 0.63 | 0.85 | 23 | empty |
| 5 | 326 | 0.55 | 0.75 | 43 | empty |
Interfaces
4 interfaces between chains.
- A–D · 1384 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1299 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 724 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 368 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4WQ5 · YgjD(V85E)-YeaZ heterodimer in complex with ATP · the same entry in another collection · chain D against D, TM-score 1.00
- P05852 · AlphaFold monomer V2.0 prediction for tRNA N6-adenosine threonylcarbamoyltransferase… · a predicted model of the same protein · chain A against A, TM-score 1.00
- P76256 · AlphaFold monomer V2.0 prediction for tRNA threonylcarbamoyladenosine biosynthesis… · a predicted model of the same protein · chain C 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 P05852
- Every structure of UniProt P76256
- Elsewhere: RCSB PDB 4WQ5 · PDBe 4WQ5 · UniProt P05852 · UniProt P76256
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