Research workbench
Two distinct conformational states of glyrs captured in crystal lattice
Analyse Two distinct conformational states of glyrs captured in crystal lattice in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QEI
- Type
- protein + RNA
- Length
- 631 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycine--tRNA ligase; TRNA-gly-ccc-2-2
- EC
- 6.1.1.14
- UniProt
- P41250
- Ligands
- AMP
- Pockets
- 11 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycine--tRNA ligase (EC 6.1.1.14) | protein | 562 | 36% helix, 27% strand | P41250 |
| C | TRNA-gly-ccc-2-2 | rna | 69 | — | — |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 745 | 0.70 | 0.78 | 40 | empty |
| 2 | 730 | 0.69 | 0.77 | 39 | empty |
| 3 | 279 | 0.60 | 0.80 | 23 | empty |
| 4 | 226 | 0.55 | 0.78 | 36 | AMP |
| 5 | 106 | 0.51 | 0.81 | 26 | empty |
Interfaces
1 interface between chains.
- A–C · 1513 Ų buried · 37 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4QEI · Two distinct conformational states of GlyRS captured in crystal lattice · 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 0.90
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 P41250
- Elsewhere: RCSB PDB 4QEI · PDBe 4QEI · UniProt P41250
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