MolNFT v1 · #1618 · protein
Glycyl-tRNA synthetase from thermus thermophilus complexed with ATP
1B76 · Glycine--tRNA ligase: “Glycyl-tRNA synthetase from thermus thermophilus complexed with ATP”. X-ray diffraction, 1 ligand (ATP), 5 pockets (best druggability 0.81). MolNFT v1 #1618 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1B76
- 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
- ATP
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glycine--tRNA ligase (EC 6.1.1.14) | protein | 442 | 32% helix, 29% strand | P56206 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1168 | 0.81 | 0.82 | 74 | empty |
| 2 | 391 | 0.68 | 0.81 | 40 | ATP |
| 3 | 418 | 0.65 | 0.78 | 50 | ATP |
| 4 | 170 | 0.45 | 0.75 | 29 | empty |
| 5 | 78 | 0.42 | 0.80 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 3589 Ų buried · 52 hydrogen bonds · protein-protein
Compared structures
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 1B76 · PDBe 1B76 · UniProt P56206
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