MolNFT v1 · #100909 · protein
D-aminoacyl-tRNA deacylase (dtd) from plasmodium falciparum in complex with D-tyrosyl-3'-aminoadenosine at 1.86 ångström resolution
4NBI · D-tyrosyl-TRNA(TYR) deacylase: “D-aminoacyl-tRNA deacylase (dtd) from plasmodium falciparum in complex with D-tyrosyl-3'-aminoadenosine at…”. X-ray diffraction, 1 ligand (D3Y), 4 pockets (best druggability 0.56). MolNFT v1 #100909…
- PDB
- 4NBI
- Type
- protein
- Length
- 314 residues
- Chains
- 2
- 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
- 4 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 163 | 25% helix, 37% strand | Q8IIS0 |
| B | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 151 | 25% helix, 37% strand | Q8IIS0 |
Ligands and binding sites
- D3Y · 3'-deoxy-3'-(D-tyrosylamino)adenosine · ligand · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.56 | 0.84 | 22 | empty |
| 2 | 181 | 0.55 | 0.80 | 28 | D3Y |
| 3 | 176 | 0.53 | 0.79 | 28 | D3Y |
| 4 | 105 | 0.53 | 0.83 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1932 Ų buried · 47 hydrogen bonds · protein-protein
Compared structures
- 4NBI · D-aminoacyl-tRNA deacylase (DTD) from Plasmodium falciparum in complex with… · the same entry in another collection · chain B against B, 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 4NBI · PDBe 4NBI · UniProt Q8IIS0
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