Research workbench
Crystal structure of human glycyl-tRNA synthetase (glyrs) in complex with gly-AMP analog
Analyse Crystal structure of human glycyl-tRNA synthetase (glyrs) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZT8
- Type
- protein
- Length
- 530 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycyl-tRNA synthetase
- EC
- 6.1.1.14
- UniProt
- P41250
- Ligands
- DRV
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycyl-tRNA synthetase (EC 6.1.1.14) | protein | 530 | 36% helix, 22% strand | P41250 |
Ligands and binding sites
- DRV · [(2S,3R,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (aminoacetyl)sulfamate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1039 | 0.81 | 0.82 | 79 | DRV |
| 2 | 93 | 0.51 | 0.82 | 18 | empty |
| 3 | 90 | 0.38 | 0.76 | 25 | empty |
| 4 | 62 | 0.33 | 0.76 | 14 | empty |
| 5 | 81 | 0.30 | 0.72 | 20 | empty |
Compared structures
- 2ZT8 · Crystal structure of human Glycyl-tRNA synthetase (GlyRS) in complex with Gly-AMP analog · the same entry in another collection · chain A against A, TM-score 1.00
- P41250 · AlphaFold monomer V2.0 prediction for glycine--tRNA ligase (P41250) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 P41250
- Elsewhere: RCSB PDB 2ZT8 · PDBe 2ZT8 · UniProt P41250
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