Research workbench
Phers in complex with compound 3A
Analyse Phers in complex with compound 3A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4P74
- Type
- protein
- Length
- 2,061 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phenylalanine--tRNA ligase beta subunit; Phenylalanine--tRNA ligase alpha subunit
- EC
- 6.1.1.20
- UniProt
- Q9I0A4, Q9I0A3
- Ligands
- 2U9
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phenylalanine--tRNA ligase beta subunit (EC 6.1.1.20) | protein | 791 | 27% helix, 30% strand | Q9I0A4 |
| C | Phenylalanine--tRNA ligase alpha subunit (EC 6.1.1.20) | protein | 235 | 32% helix, 29% strand | Q9I0A3 |
| D | Phenylalanine--tRNA ligase alpha subunit (EC 6.1.1.20) | protein | 244 | 31% helix, 27% strand | Q9I0A3 |
Ligands and binding sites
- 2U9 · N-[(3S)-1,1-dioxidotetrahydrothiophen-3-yl]-2-[(4-methylphenoxy)methyl]-1,3-thiazole-4-carboxamide · ligand · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 801 | 0.85 | 0.88 | 73 | empty |
| 2 | 357 | 0.77 | 0.88 | 33 | empty |
| 3 | 1193 | 0.75 | 0.78 | 104 | 2U9 |
| 4 | 697 | 0.73 | 0.79 | 69 | 2U9 |
| 5 | 252 | 0.73 | 0.87 | 29 | empty |
Interfaces
6 interfaces between chains.
- B–D · 3571 Ų buried · 60 hydrogen bonds · protein-protein
- A–C · 3504 Ų buried · 58 hydrogen bonds · protein-protein
- A–D · 2003 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 1990 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1545 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 4P74 · PheRS in complex with compound 3a · the same entry in another collection · chain A against A, TM-score 1.00
- Q9I0A3 · AlphaFold monomer V2.0 prediction for phenylalanine--tRNA ligase alpha subunit (Q9I0A3) · a predicted model of the same protein · chain C against A, TM-score 0.95
- Q9I0A4 · AlphaFold monomer V2.0 prediction for phenylalanine--tRNA ligase beta subunit (Q9I0A4) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 Q9I0A4
- Every structure of UniProt Q9I0A3
- Elsewhere: RCSB PDB 4P74 · PDBe 4P74 · UniProt Q9I0A4 · UniProt Q9I0A3
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