Research workbench
Crystal structure of D-tyr-TRNA(TYR) deacylase from plasmodium falciparum
Analyse Crystal structure of D-tyr-TRNA(TYR) deacylase from plasmodium falciparum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KNF
- Type
- protein
- Length
- 909 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
- Pockets
- 11 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 25% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 151 | 21% helix, 40% strand | Q8IIS0 |
| B, F | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 152 | 28% helix, 37% strand | Q8IIS0 |
| C | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 150 | 30% helix, 40% strand | Q8IIS0 |
| D | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 154 | 25% helix, 45% strand | Q8IIS0 |
| E | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 150 | 23% helix, 37% strand | Q8IIS0 |
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 521 | 0.72 | 0.81 | 56 | empty |
| 2 | 733 | 0.70 | 0.77 | 59 | empty |
| 3 | 159 | 0.59 | 0.83 | 26 | empty |
| 4 | 209 | 0.55 | 0.79 | 31 | empty |
| 5 | 141 | 0.55 | 0.81 | 31 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1930 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 1856 Ų buried · 42 hydrogen bonds · protein-protein
- E–F · 1797 Ų buried · 39 hydrogen bonds · protein-protein
- B–F · 424 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 383 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3KNF · Crystal structure of D-Tyr-tRNA(Tyr) deacylase from Plasmodium falciparum · 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 3KNF · PDBe 3KNF · UniProt Q8IIS0
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