MolNFT v1 · #122985 · protein
D-aminoacyl-tRNA deacylase (dtd) from plasmodium falciparum in complex with glycyl-3'-aminoadenosine at 2.10 ångström resolution
5J61 · D-tyrosyl-TRNA(TYR) deacylase: “D-aminoacyl-tRNA deacylase (dtd) from plasmodium falciparum in complex with glycyl-3'-aminoadenosine at 2.10…”. X-ray diffraction, 1 ligand (A3G), 13 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 5J61
- Type
- protein
- Length
- 1,214 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
- A3G
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 7 distinct chains · 25% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 151 | 25% helix, 38% strand | Q8IIS0 |
| B | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 152 | 25% helix, 38% strand | Q8IIS0 |
| C | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 153 | 27% helix, 39% strand | Q8IIS0 |
| D, F | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 152 | 25% helix, 39% strand | Q8IIS0 |
| E | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 152 | 27% helix, 38% strand | Q8IIS0 |
| G | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 152 | 23% helix, 38% strand | Q8IIS0 |
| H | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 150 | 23% helix, 43% strand | Q8IIS0 |
Ligands and binding sites
- A3G · 3'-deoxy-3'-(glycylamino)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
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1078 | 0.81 | 0.82 | 94 | A3G |
| 2 | 642 | 0.73 | 0.80 | 62 | empty |
| 3 | 508 | 0.71 | 0.81 | 56 | empty |
| 4 | 199 | 0.60 | 0.82 | 29 | empty |
| 5 | 225 | 0.60 | 0.81 | 30 | empty |
Interfaces
11 interfaces between chains.
- G–H · 1991 Ų buried · 52 hydrogen bonds · protein-protein
- A–B · 1982 Ų buried · 47 hydrogen bonds · protein-protein
- E–F · 1964 Ų buried · 51 hydrogen bonds · protein-protein
- C–D · 1936 Ų buried · 50 hydrogen bonds · protein-protein
- B–F · 370 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5J61 · 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 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 5J61 · PDBe 5J61 · UniProt Q8IIS0
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