MolNFT v1 · #69361 · protein
Dtd from plasmodium falciparum in complex with D-arginine
3KO9 · D-tyrosyl-TRNA(TYR) deacylase: “Dtd from plasmodium falciparum in complex with D-arginine”. X-ray diffraction, 1 ligand (DAR), 11 pockets (best druggability 0.67). MolNFT v1 #69361 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3KO9
- Type
- protein
- Length
- 910 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
- DAR
- Pockets
- 11 · best druggability 0.67
Structure
x-ray diffraction · 6 distinct chains · 24% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 149 | 23% helix, 43% strand | Q8IIS0 |
| B | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 151 | 26% helix, 42% strand | Q8IIS0 |
| C | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 159 | 24% helix, 38% strand | Q8IIS0 |
| D | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 151 | 25% helix, 46% strand | Q8IIS0 |
| E | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 150 | 23% helix, 43% strand | Q8IIS0 |
| F | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 150 | 23% helix, 45% strand | Q8IIS0 |
Ligands and binding sites
- DAR · D-arginine · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 207 | 0.67 | 0.85 | 31 | empty |
| 2 | 480 | 0.64 | 0.77 | 60 | empty |
| 3 | 170 | 0.55 | 0.80 | 31 | empty |
| 4 | 165 | 0.53 | 0.79 | 29 | empty |
| 5 | 177 | 0.52 | 0.78 | 27 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1903 Ų buried · 48 hydrogen bonds · protein-protein
- E–F · 1821 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 1774 Ų buried · 45 hydrogen bonds · protein-protein
- B–E · 726 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 532 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
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 3KO9 · PDBe 3KO9 · UniProt Q8IIS0
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