Research workbench
Crystal structure of B. stearothermophilus tryptophanyl tRNA synthetase in complex with adenosine tetraphosphate
Analyse Crystal structure of B. stearothermophilus tryptophanyl tRNA synthetase in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OV4
- Type
- protein
- Length
- 328 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptophanyl-tRNA synthetase
- EC
- 6.1.1.2
- UniProt
- P00953
- Ligands
- AQP, ANL, CS
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 57% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophanyl-tRNA synthetase (EC 6.1.1.2) | protein | 328 | 57% helix, 8% strand | P00953 |
Ligands and binding sites
- AQP · Adenosine-5'-tetraphosphate · ligand · chains A
- ANL · Aniline · ligand · chains A
- CS · Cesium ion · metal · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 382 | 0.75 | 0.85 | 53 | AQP, ANL |
| 2 | 84 | 0.35 | 0.75 | 15 | empty |
Compared structures
- 2OV4 · Crystal structure of B. stearothermophilus tryptophanyl tRNA synthetase in complex with… · 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 0.95
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 2OV4 · PDBe 2OV4 · UniProt P00953
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