MolNFT v1 · #15915 · protein
Crystal structure of prolyl-tRNA synthetase from methanocaldococcus janaschii
1NJ8 · Proline-tRNA synthetase: “Crystal structure of prolyl-tRNA synthetase from methanocaldococcus janaschii”. X-ray diffraction, 17 pockets (best druggability 0.80). MolNFT v1 #15915 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 1NJ8
- Type
- protein
- Length
- 1,824 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proline-tRNA synthetase
- EC
- 6.1.1.15
- UniProt
- Q58635
- Pockets
- 17 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Proline-tRNA synthetase (EC 6.1.1.15) | protein | 456 | 36% helix, 27% strand | Q58635 |
Pockets
17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 745 | 0.80 | 0.83 | 67 | empty |
| 2 | 413 | 0.78 | 0.87 | 42 | empty |
| 3 | 888 | 0.77 | 0.80 | 77 | empty |
| 4 | 631 | 0.74 | 0.81 | 52 | empty |
| 5 | 547 | 0.74 | 0.82 | 44 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2399 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 2390 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 681 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 423 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1NJ8 · Crystal Structure of Prolyl-tRNA Synthetase from Methanocaldococcus janaschii · the same entry in another collection · chain A against A, TM-score 1.00
- Q58635 · AlphaFold monomer V2.0 prediction for proline--tRNA ligase (Q58635) · 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 Q58635
- Elsewhere: RCSB PDB 1NJ8 · PDBe 1NJ8 · UniProt Q58635
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