Research workbench
D-tyrosyl-TRNA(TYR) deacylase from plasmodium falciparum incomplex with ADP, obtained through soaking native enzyme crystal with the ATP
Analyse D-tyrosyl-TRNA(TYR) deacylase from plasmodium falciparum incomplex with ADP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KO3
- Type
- protein
- Length
- 922 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-tyrosyl-TRNA(TYR) deacylase
- EC
- 3.1.-.-
- UniProt
- Q8IIS0
- Ligands
- ADP
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 152 | 24% helix, 43% strand | Q8IIS0 |
| B, D, F | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 154 | 29% helix, 45% strand | Q8IIS0 |
| C | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 153 | 25% helix, 39% strand | Q8IIS0 |
| E | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 155 | 25% helix, 43% strand | Q8IIS0 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 685 | 0.78 | 0.83 | 65 | empty |
| 2 | 204 | 0.64 | 0.83 | 31 | empty |
| 3 | 133 | 0.50 | 0.79 | 25 | empty |
| 4 | 133 | 0.50 | 0.79 | 27 | empty |
| 5 | 144 | 0.49 | 0.78 | 27 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1965 Ų buried · 45 hydrogen bonds · protein-protein
- C–D · 1929 Ų buried · 47 hydrogen bonds · protein-protein
- E–F · 1924 Ų buried · 46 hydrogen bonds · protein-protein
- B–D · 397 Ų buried · 0 hydrogen bonds · protein-protein
- D–E · 231 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3KO3 · D-tyrosyl-tRNA(Tyr) deacylase from Plasmodium falciparum incomplex with ADP, obtained… · the same entry in another collection · chain F against F, TM-score 1.00
- Q8IIS0 · AlphaFold monomer V2.0 prediction for D-aminoacyl-tRNA deacylase (Q8IIS0) · a predicted model of the same protein · chain E against A, TM-score 0.99
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 Q8IIS0
- Elsewhere: RCSB PDB 3KO3 · PDBe 3KO3 · UniProt Q8IIS0
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