Research workbench
D-aminoacyl-tRNA deacylase (dtd) from plasmodium falciparum in complex with D-tyrosyl-3'-aminoadenosine at 2.20 ångström resolution
Analyse D-aminoacyl-tRNA deacylase (dtd) from plasmodium falciparum in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NBJ
- Type
- protein
- Length
- 1,222 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-tyrosyl-TRNA(TYR) deacylase
- EC
- 3.1.-.-
- UniProt
- Q8IIS0
- Ligands
- D3Y
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 25% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 154 | 25% helix, 42% strand | Q8IIS0 |
| B, D | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 154 | 27% helix, 43% strand | Q8IIS0 |
| C, E, H | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 152 | 24% helix, 43% strand | Q8IIS0 |
| F | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 153 | 25% helix, 42% strand | Q8IIS0 |
| G | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 151 | 23% helix, 38% strand | Q8IIS0 |
Ligands and binding sites
- D3Y · 3'-deoxy-3'-(D-tyrosylamino)adenosine · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1174 | 0.77 | 0.79 | 92 | empty |
| 2 | 709 | 0.74 | 0.80 | 67 | empty |
| 3 | 502 | 0.65 | 0.77 | 58 | D3Y |
| 4 | 199 | 0.57 | 0.80 | 31 | empty |
| 5 | 182 | 0.57 | 0.80 | 27 | D3Y |
Interfaces
13 interfaces between chains.
- G–H · 1974 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 1949 Ų buried · 46 hydrogen bonds · protein-protein
- E–F · 1941 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 1940 Ų buried · 48 hydrogen bonds · protein-protein
- A–D · 653 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4NBJ · D-aminoacyl-tRNA deacylase (DTD) from Plasmodium falciparum in complex with… · the same entry in another collection · chain H against H, TM-score 1.00
- Q8IIS0 · AlphaFold monomer V2.0 prediction for D-aminoacyl-tRNA deacylase (Q8IIS0) · a predicted model of the same protein · chain C 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 4NBJ · PDBe 4NBJ · UniProt Q8IIS0
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