Research workbench
Crystal structure of glutamyl-tRNA synthetase (gltx) from stenotrophomonas maltophilia
Analyse Crystal structure of glutamyl-tRNA synthetase (gltx) from stenotrophomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K86
- Type
- protein
- Length
- 923 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate--tRNA ligase
- EC
- 6.1.1.17
- UniProt
- B2FHI7
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate--tRNA ligase (EC 6.1.1.17) | protein | 459 | 50% helix, 12% strand | B2FHI7 |
| B | Glutamate--tRNA ligase (EC 6.1.1.17) | protein | 464 | 51% helix, 12% strand | B2FHI7 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1124 | 0.74 | 0.77 | 87 | ACT |
| 2 | 635 | 0.70 | 0.78 | 51 | ACT |
| 3 | 373 | 0.61 | 0.77 | 36 | empty |
| 4 | 365 | 0.56 | 0.74 | 41 | empty |
| 5 | 120 | 0.36 | 0.72 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 896 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 7K86 · Crystal Structure of Glutamyl-tRNA synthetase (gltX) from Stenotrophomonas maltophilia · the same entry in another collection · chain A against A, TM-score 1.00
- B2FHI7 · AlphaFold monomer V2.0 prediction for glutamate--tRNA ligase (B2FHI7) · a predicted model of the same protein · chain A 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 B2FHI7
- Elsewhere: RCSB PDB 7K86 · PDBe 7K86 · UniProt B2FHI7
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