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Crystal structure of tryptophanyl-tRNA synthetase from bacillus stearothermophilus in complex with chuangxinmycin
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
- 7CMS
- Type
- protein
- Length
- 653 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
- P00953
- Ligands
- 9E0, PO4
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan--tRNA ligase (EC 6.1.1.2) | protein | 328 | 57% helix, 8% strand | P00953 |
| B | Tryptophan--tRNA ligase (EC 6.1.1.2) | protein | 325 | 58% helix, 9% strand | P00953 |
Ligands and binding sites
- 9E0 · (5~{S},6~{R})-5-methyl-7-thia-2-azatricyclo[6.3.1.0^{4, 12}]dodeca-1(12),3,8,10-tetraene-6-carboxylic acid · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 587 | 0.79 | 0.84 | 55 | 9E0, PO4 |
| 2 | 590 | 0.74 | 0.81 | 50 | 9E0, PO4 |
| 3 | 117 | 0.53 | 0.81 | 19 | empty |
| 4 | 52 | 0.37 | 0.80 | 18 | empty |
| 5 | 68 | 0.34 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2318 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 7CMS · 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 0.97
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 7CMS · PDBe 7CMS · UniProt P00953
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