Research workbench
Crystal structure at 2.6A resolution of phenylalanyl-tRNA synthetase complexed with phenylalanyl-adenylate in the presence of manganese
Analyse Crystal structure at 2.6A resolution of phenylalanyl-tRNA synthetase complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JJC
- Type
- protein
- Length
- 1,051 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phenylalanyl-tRNA synthetase alpha chain; Phenylalanyl-tRNA synthetase beta chain
- EC
- 6.1.1.20
- UniProt
- Q5SGX2, Q5SGX1
- Ligands
- FA5, MN, SO4
- Pockets
- 16 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phenylalanyl-tRNA synthetase alpha chain (EC 6.1.1.20) | protein | 266 | 33% helix, 27% strand | Q5SGX2 |
| B | Phenylalanyl-tRNA synthetase beta chain (EC 6.1.1.20) | protein | 785 | 28% helix, 28% strand | Q5SGX1 |
Ligands and binding sites
- FA5 · Adenosine-5'-[phenylalaninyl-phosphate] · ligand · chains A
- MN · Manganese (II) ion · metal · chains A, B
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 71 | 0.71 | 0.97 | 19 | empty |
| 2 | 659 | 0.71 | 0.78 | 67 | FA5 |
| 3 | 406 | 0.70 | 0.82 | 49 | empty |
| 4 | 408 | 0.64 | 0.78 | 43 | empty |
| 5 | 400 | 0.63 | 0.77 | 46 | MN |
Interfaces
1 interface between chains.
- A–B · 4296 Ų buried · 67 hydrogen bonds · protein-protein
Compared structures
- 1JJC · Crystal structure at 2.6A resolution of phenylalanyl-tRNA synthetase complexed with… · 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 1JJC · PDBe 1JJC · UniProt Q5SGX2 · UniProt Q5SGX1
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