Research workbench
Crystal structure of prolyl-tRNA synthetase from methanothermobacter thermautotrophicus bound to alanine sulfamoyl adenylate
Analyse Crystal structure of prolyl-tRNA synthetase from methanothermobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NJ6
- Type
- protein
- Length
- 463 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proline-tRNA synthetase
- EC
- 6.1.1.15
- UniProt
- O26708
- Ligands
- A5A, ZN, MG
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proline-tRNA synthetase (EC 6.1.1.15) | protein | 463 | 36% helix, 29% strand | O26708 |
Ligands and binding sites
- A5A · 5'-O-(N-(L-alanyl)-sulfamoyl)adenosine · ligand · chains A
- ZN · Zinc ion · metal · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 383 | 0.72 | 0.83 | 42 | A5A |
| 2 | 138 | 0.48 | 0.78 | 26 | empty |
| 3 | 80 | 0.33 | 0.74 | 20 | empty |
| 4 | 69 | 0.29 | 0.72 | 13 | empty |
Compared structures
- 1NJ6 · Crystal structure of Prolyl-tRNA Synthetase from Methanothermobacter thermautotrophicus… · the same entry in another collection · chain A against A, TM-score 1.00
- O26708 · AlphaFold monomer V2.0 prediction for proline--tRNA ligase (O26708) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 O26708
- Elsewhere: RCSB PDB 1NJ6 · PDBe 1NJ6 · UniProt O26708
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