MolNFT v1 · #111008 · protein
Crystal structure of E. COLI ygjd-yeaz heterodimer in complex with ADP
4YDU · TRNA N6-adenosine threonylcarbamoyltransferase: “Crystal structure of E. COLI ygjd-yeaz heterodimer in complex with ADP”. X-ray diffraction, 3 ligands (ADP, MG, FE), 9 pockets (best druggability 0.74). MolNFT v1 #111008 on…
- PDB
- 4YDU
- Type
- protein
- Length
- 1,133 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
- ADP, MG, FE
- Pockets
- 9 · best druggability 0.74
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 | 336 | 46% helix, 20% strand | P05852 |
| B | TRNA N6-adenosine threonylcarbamoyltransferase (EC 2.6.99.4) | protein | 338 | 47% helix, 20% strand | P05852 |
| C | TRNA threonylcarbamoyladenosine biosynthesis protein tsab | protein | 230 | 36% helix, 29% strand | P76256 |
| D | TRNA threonylcarbamoyladenosine biosynthesis protein tsab | protein | 229 | 35% helix, 31% strand | P76256 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains A, B
- FE · Fe (III) ion · metal · 2 copies · chains A, B
- ACT · Acetate ion · additive · 13 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 794 | 0.74 | 0.79 | 77 | ADP, MG |
| 2 | 620 | 0.73 | 0.80 | 71 | ADP, MG, FE |
| 3 | 268 | 0.67 | 0.83 | 41 | empty |
| 4 | 450 | 0.65 | 0.78 | 47 | empty |
| 5 | 177 | 0.44 | 0.74 | 31 | ADP, ACT |
Interfaces
4 interfaces between chains.
- A–C · 1430 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 1411 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 639 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 414 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4YDU · Crystal structure of E. coli YgjD-YeaZ heterodimer in complex with ADP · 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 D against A, TM-score 0.97
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 4YDU · PDBe 4YDU · UniProt P05852 · UniProt P76256
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