MolNFT v1 · #18748 · protein
Phenylalanyl-tRNA synthetase from thermus thermophilus
1PYS: “Phenylalanyl-tRNA synthetase from thermus thermophilus”. X-ray diffraction, 1 ligand (MG), 14 pockets (best druggability 0.70). MolNFT v1 #18748 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1PYS
- Type
- protein
- Length
- 1,051 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phenylalanyl-tRNA synthetase
- EC
- 6.1.1.20
- UniProt
- Q5SGX2, Q5SGX1
- Ligands
- MG
- Pockets
- 14 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phenylalanyl-tRNA synthetase (EC 6.1.1.20) | protein | 266 | 32% helix, 27% strand | Q5SGX2 |
| B | Phenylalanyl-tRNA synthetase (EC 6.1.1.20) | protein | 785 | 28% helix, 29% strand | Q5SGX1 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 533 | 0.70 | 0.79 | 53 | empty |
| 2 | 424 | 0.70 | 0.81 | 50 | empty |
| 3 | 591 | 0.68 | 0.77 | 46 | empty |
| 4 | 342 | 0.57 | 0.76 | 42 | MG |
| 5 | 116 | 0.56 | 0.84 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 4387 Ų buried · 65 hydrogen bonds · protein-protein
Compared structures
- 1PYS · Phenylalanyl-tRNA synthetase from thermus thermophilus · the same entry in another collection · chain A against A, TM-score 1.00
- Q5SGX1 · AlphaFold monomer V2.0 prediction for phenylalanine--tRNA ligase beta subunit (Q5SGX1) · a predicted model of the same protein · chain B against A, TM-score 0.97
- Q5SGX2 · AlphaFold monomer V2.0 prediction for phenylalanine--tRNA ligase alpha subunit (Q5SGX2) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q5SGX2
- Every structure of UniProt Q5SGX1
- Elsewhere: RCSB PDB 1PYS · PDBe 1PYS · UniProt Q5SGX2 · UniProt Q5SGX1
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