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X-ray crystallographic structure of E. COLI K-12 glycyl-tRNA synthetase alpha subunit (glyq)
Analyse X-ray crystallographic structure of E. COLI K-12 glycyl-tRNA synthetase alpha… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QCF
- Type
- protein
- Length
- 1,137 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycine--tRNA ligase alpha subunit
- EC
- 6.1.1.14
- UniProt
- P00960
- Pockets
- 17 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycine--tRNA ligase alpha subunit (EC 6.1.1.14) | protein | 283 | 43% helix, 23% strand | P00960 |
| B | Glycine--tRNA ligase alpha subunit (EC 6.1.1.14) | protein | 285 | 44% helix, 25% strand | P00960 |
| C | Glycine--tRNA ligase alpha subunit (EC 6.1.1.14) | protein | 282 | 45% helix, 23% strand | P00960 |
| D | Glycine--tRNA ligase alpha subunit (EC 6.1.1.14) | protein | 287 | 43% helix, 24% strand | P00960 |
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1145 | 0.87 | 0.87 | 93 | empty |
| 2 | 957 | 0.81 | 0.83 | 104 | empty |
| 3 | 213 | 0.63 | 0.83 | 38 | empty |
| 4 | 230 | 0.62 | 0.81 | 31 | empty |
| 5 | 232 | 0.57 | 0.78 | 27 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2479 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 794 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 787 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 24 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 22 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7QCF · X-ray crystallographic structure of E. coli K-12 glycyl-tRNA synthetase alpha subunit… · the same entry in another collection · chain D against D, TM-score 1.00
- P00960 · AlphaFold monomer V2.0 prediction for glycine--tRNA ligase alpha subunit (P00960) · a predicted model of the same protein · chain C against A, TM-score 0.90
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 P00960
- Elsewhere: RCSB PDB 7QCF · PDBe 7QCF · UniProt P00960
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