Research workbench
Phers from staphylococcus haemolyticus- rational protein engineering and inhibitor studies
Analyse Phers from staphylococcus haemolyticus- rational protein engineering and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2RHQ
- Type
- protein
- Length
- 1,060 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
- Q4L5E3, Q4L5E4
- Ligands
- GAX, ZN
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phenylalanyl-tRNA synthetase alpha chain (EC 6.1.1.20) | protein | 270 | 29% helix, 24% strand | Q4L5E3 |
| B | Phenylalanyl-tRNA synthetase beta chain (EC 6.1.1.20) | protein | 790 | 29% helix, 30% strand | Q4L5E4 |
Ligands and binding sites
- GAX · 1-{3-[(4-pyridin-2-ylpiperazin-1-yl)sulfonyl]phenyl}-3-(1,3-thiazol-2-yl)urea · ligand · chains A
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 426 | 0.81 | 0.89 | 45 | empty |
| 2 | 693 | 0.70 | 0.77 | 54 | GAX |
| 3 | 420 | 0.65 | 0.78 | 60 | empty |
| 4 | 303 | 0.62 | 0.79 | 33 | empty |
| 5 | 57 | 0.51 | 0.87 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 3797 Ų buried · 60 hydrogen bonds · protein-protein
Compared structures
- 2RHQ · PheRS from Staphylococcus haemolyticus- rational protein engineering and inhibitor studies · the same entry in another collection · chain A against A, TM-score 1.00
- Q4L5E4 · AlphaFold monomer V2.0 prediction for phenylalanine--tRNA ligase beta subunit (Q4L5E4) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q4L5E3 · AlphaFold monomer V2.0 prediction for phenylalanine--tRNA ligase alpha subunit (Q4L5E3) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q4L5E3
- Every structure of UniProt Q4L5E4
- Elsewhere: RCSB PDB 2RHQ · PDBe 2RHQ · UniProt Q4L5E3 · UniProt Q4L5E4
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