Research workbench
Leishmania donovani tyrosyl-tRNA synthetase in complex with nanobody and inhibitor
Analyse Leishmania donovani tyrosyl-tRNA synthetase in complex with nanobody and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5USF
- Type
- protein
- Length
- 1,600 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosyl-tRNA synthetase, putative; Immunoglobulin heavy chain variable region
- UniProt
- E9BC28
- Ligands
- YSA
- Pockets
- 18 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosyl-tRNA synthetase, putative | protein | 682 | 51% helix, 10% strand | E9BC28 |
| B | Tyrosyl-tRNA synthetase, putative | protein | 680 | 52% helix, 10% strand | E9BC28 |
| C | Immunoglobulin heavy chain variable region | protein | 118 | 8% helix, 53% strand | — |
| D | Immunoglobulin heavy chain variable region | protein | 120 | 8% helix, 53% strand | — |
Ligands and binding sites
- YSA · 5'-O-[N-(L-tyrosyl)sulfamoyl]adenosine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 764 | 0.77 | 0.81 | 66 | YSA |
| 2 | 615 | 0.76 | 0.82 | 52 | YSA |
| 3 | 607 | 0.73 | 0.80 | 49 | empty |
| 4 | 511 | 0.69 | 0.79 | 43 | empty |
| 5 | 482 | 0.67 | 0.78 | 45 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1043 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 1017 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 416 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 340 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5USF · Leishmania donovani tyrosyl-tRNA synthetase in complex with nanobody and inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
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 E9BC28
- Elsewhere: RCSB PDB 5USF · PDBe 5USF · UniProt E9BC28
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