Research workbench
Crystal structure of D-tyr-TRNA(TYR) deacylase from plasmodium falciparum in complex with ADP
Analyse Crystal structure of D-tyr-TRNA(TYR) deacylase from plasmodium falciparum in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KO4
- Type
- protein
- Length
- 906 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
- 12 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 26% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 151 | 25% helix, 41% strand | Q8IIS0 |
| B | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 152 | 27% helix, 44% strand | Q8IIS0 |
| C | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 151 | 27% helix, 38% strand | Q8IIS0 |
| D, F | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 151 | 25% helix, 42% strand | Q8IIS0 |
| E | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 150 | 27% helix, 39% strand | Q8IIS0 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 796 | 0.78 | 0.82 | 66 | empty |
| 2 | 193 | 0.61 | 0.83 | 29 | empty |
| 3 | 163 | 0.56 | 0.81 | 32 | empty |
| 4 | 180 | 0.53 | 0.79 | 30 | empty |
| 5 | 142 | 0.53 | 0.80 | 27 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1970 Ų buried · 46 hydrogen bonds · protein-protein
- C–D · 1960 Ų buried · 51 hydrogen bonds · protein-protein
- E–F · 1948 Ų buried · 48 hydrogen bonds · protein-protein
- B–D · 383 Ų buried · 1 hydrogen bond · protein-protein
- D–F · 304 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3KO4 · Crystal structure of D-Tyr-tRNA(Tyr) deacylase from Plasmodium falciparum in complex with… · 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 B 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 3KO4 · PDBe 3KO4 · UniProt Q8IIS0
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