Research workbench
Dtd from plasmodium falciparum in complex with D-glutamic acid
Analyse Dtd from plasmodium falciparum in complex with D-glutamic acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KOB
- Type
- protein
- Length
- 911 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
- DGL
- Pockets
- 10 · best druggability 0.71
Structure
x-ray diffraction · 6 distinct chains · 25% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 150 | 29% helix, 38% strand | Q8IIS0 |
| B | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 151 | 25% helix, 44% strand | Q8IIS0 |
| C | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 160 | 24% helix, 36% strand | Q8IIS0 |
| D | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 151 | 25% helix, 41% strand | Q8IIS0 |
| E | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 149 | 26% helix, 38% strand | Q8IIS0 |
| F | D-tyrosyl-TRNA(TYR) deacylase (EC 3.1.-.-) | protein | 150 | 23% helix, 35% strand | Q8IIS0 |
Ligands and binding sites
- DGL · D-glutamic acid · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 436 | 0.71 | 0.82 | 53 | empty |
| 2 | 379 | 0.59 | 0.76 | 48 | empty |
| 3 | 247 | 0.58 | 0.79 | 33 | empty |
| 4 | 176 | 0.55 | 0.80 | 30 | empty |
| 5 | 179 | 0.54 | 0.79 | 27 | DGL |
Interfaces
7 interfaces between chains.
- A–B · 1924 Ų buried · 47 hydrogen bonds · protein-protein
- E–F · 1834 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 1826 Ų buried · 36 hydrogen bonds · protein-protein
- A–F · 685 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 440 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3KOB · DTD from Plasmodium falciparum in complex with D-Glutamic acid · 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 A 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 3KOB · PDBe 3KOB · UniProt Q8IIS0
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