Research workbench
Crystal structure of tryptophanyl-tRNA synthetase from bacillus stearothermophilus in complex with 05E6 and ATP
Analyse Crystal structure of tryptophanyl-tRNA synthetase from bacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EER
- Type
- protein
- Length
- 1,304 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptophan--tRNA ligase
- EC
- 6.1.1.2
- UniProt
- P00953
- Ligands
- ATP, ZCW
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 56% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Tryptophan--tRNA ligase (EC 6.1.1.2) | protein | 326 | 56% helix, 9% strand | P00953 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- ZCW · 2-(1H-indol-3-yl)ethanol · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1012 | 0.86 | 0.87 | 111 | ATP, ZCW |
| 2 | 1003 | 0.85 | 0.86 | 116 | ATP, ZCW |
| 3 | 448 | 0.76 | 0.85 | 62 | ATP, ZCW |
| 4 | 442 | 0.75 | 0.85 | 56 | ATP, ZCW |
| 5 | 167 | 0.50 | 0.78 | 29 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2165 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 706 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 706 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 275 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 273 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 7EER · Crystal structure of Tryptophanyl-tRNA synthetase from Bacillus stearothermophilus in… · the same entry in another collection · chain A against A, TM-score 1.00
- P00953 · AlphaFold monomer V2.0 prediction for tryptophan--tRNA ligase (P00953) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P00953
- Elsewhere: RCSB PDB 7EER · PDBe 7EER · UniProt P00953
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