Research workbench
Crystal structure of tryptophanyl-tRNA synthetase from escherichia COLI complexed with AMP and tryptophan
Analyse Crystal structure of tryptophanyl-tRNA synthetase from escherichia COLI… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V0I
- Type
- protein
- Length
- 646 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptophan--tRNA ligase
- EC
- 6.1.1.2
- UniProt
- P67589
- Ligands
- AMP, TRP
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan--tRNA ligase (EC 6.1.1.2) | protein | 321 | 55% helix, 10% strand | P67589 |
| B | Tryptophan--tRNA ligase (EC 6.1.1.2) | protein | 325 | 56% helix, 10% strand | P67589 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- TRP · Tryptophan · ligand · 2 copies · chains A, B
- FMT · Formic acid · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 619 | 0.74 | 0.80 | 60 | AMP, TRP |
| 2 | 546 | 0.72 | 0.80 | 52 | AMP, TRP |
| 3 | 93 | 0.43 | 0.78 | 15 | empty |
| 4 | 110 | 0.39 | 0.75 | 16 | empty |
| 5 | 78 | 0.35 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2497 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 5V0I · Crystal Structure of Tryptophanyl-tRNA Synthetase from Escherichia coli Complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- P67589 · AlphaFold monomer V2.0 prediction for tryptophan--tRNA ligase (P67589) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P67589
- Elsewhere: RCSB PDB 5V0I · PDBe 5V0I · UniProt P67589
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