Research workbench
Crystal Structure of tryptophanyl-tRNA synthetase from Mycoplasma pneumoniae
Analyse Crystal Structure of tryptophanyl-tRNA synthetase from Mycoplasma pneumoniae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YY5
- Type
- protein
- Length
- 1,362 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.55
- Source
- Mycoplasma pneumoniae
- Molecule
- Tryptophanyl-tRNA synthetase
- EC
- 6.1.1.2
- UniProt
- P75510
- Ligands
- WSA, SO4
- Pockets
- 19 · best druggability 0.77
Structure
x-ray diffraction · resolution 2.55 · 3 distinct chains · 58% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophanyl-tRNA synthetase (EC 6.1.1.2) | protein | 334 | 59% helix, 9% strand | P75510 |
| B, D | Tryptophanyl-tRNA synthetase (EC 6.1.1.2) | protein | 346 | 56% helix, 9% strand | P75510 |
| C | Tryptophanyl-tRNA synthetase (EC 6.1.1.2) | protein | 336 | 58% helix, 9% strand | P75510 |
Ligands and binding sites
- WSA · 5'-O-[(L-tryptophylamino)sulfonyl]adenosine · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 576 | 0.77 | 0.84 | 57 | SO4, WSA |
| 2 | 575 | 0.75 | 0.82 | 55 | SO4, WSA |
| 3 | 578 | 0.74 | 0.81 | 55 | SO4, WSA |
| 4 | 506 | 0.74 | 0.82 | 50 | SO4, WSA |
| 5 | 259 | 0.52 | 0.76 | 35 | empty |
Interfaces
2 interfaces between chains.
- C–D · 2460 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 2409 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 2YY5 · Crystal structure of tryptophanyl-tRNA synthetase from mycoplasma pneumoniae · the same entry in another collection · chain A against A, TM-score 1.00
- P75510 · AlphaFold monomer V2.0 prediction for tryptophan--tRNA ligase (P75510) · 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 P75510
- Elsewhere: RCSB PDB 2YY5 · PDBe 2YY5 · UniProt P75510
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