MolNFT v1 · #7768 · protein
Glycyl-tRNA synthetase from thermus thermophilus complexed with glycyl-adenylate
1GGM · Glycine--tRNA ligase: “Glycyl-tRNA synthetase from thermus thermophilus complexed with glycyl-adenylate”. X-ray diffraction, 1 ligand (GAP), 6 pockets (best druggability 0.81). MolNFT v1 #7768 on GenesisL1: 3D structure, binding…
- PDB
- 1GGM
- Type
- protein
- Length
- 884 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycine--tRNA ligase
- EC
- 6.1.1.14
- UniProt
- P56206
- Ligands
- GAP
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glycine--tRNA ligase (EC 6.1.1.14) | protein | 442 | 33% helix, 27% strand | P56206 |
Ligands and binding sites
- GAP · Glycyl-adenosine-5'-phosphate · ligand · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1080 | 0.81 | 0.83 | 76 | empty |
| 2 | 430 | 0.69 | 0.81 | 41 | GAP |
| 3 | 449 | 0.66 | 0.79 | 46 | GAP |
| 4 | 259 | 0.53 | 0.76 | 39 | empty |
| 5 | 75 | 0.49 | 0.84 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 3612 Ų buried · 55 hydrogen bonds · protein-protein
Compared structures
- 1GGM · Glycyl-tRNA synthetase from thermus thermophilus complexed with glycyl-adenylate · the same entry in another collection · chain A against A, TM-score 1.00
- P56206 · AlphaFold monomer V2.0 prediction for glycine--tRNA ligase (P56206) · 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 P56206
- Elsewhere: RCSB PDB 1GGM · PDBe 1GGM · UniProt P56206
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