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The crystal structure of phenylalanyl-tRNA synthetase from thermus thermophilus complexed with cognate trnaphe
Analyse The crystal structure of phenylalanyl-tRNA synthetase from thermus thermophilus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EIY
- Type
- protein + RNA
- Length
- 1,206 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA(PHE); Phenylalanyl-tRNA synthetase
- EC
- 6.1.1.20
- UniProt
- Q5SGX1, P27001, Q5SGX2
- Pockets
- 19 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | TRNA(PHE) | rna | 76 | — | Q5SGX1 |
| A | Phenylalanyl-tRNA synthetase (EC 6.1.1.20) | protein | 345 | 39% helix, 19% strand | P27001 |
| B | Phenylalanyl-tRNA synthetase (EC 6.1.1.20) | protein | 785 | 27% helix, 24% strand | Q5SGX2 |
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 988 | 0.76 | 0.79 | 78 | empty |
| 2 | 61 | 0.69 | 0.97 | 20 | empty |
| 3 | 733 | 0.67 | 0.76 | 30 | empty |
| 4 | 466 | 0.66 | 0.79 | 38 | empty |
| 5 | 672 | 0.66 | 0.76 | 61 | empty |
Interfaces
3 interfaces between chains.
- A–B · 4317 Ų buried · 66 hydrogen bonds · protein-protein
- C–B · 561 Ų buried · 8 hydrogen bonds · protein-nucleic
- C–A · 347 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 1EIY · The crystal structure of phenylalanyl-tRNA synthetase from thermus thermophilus complexed… · the same entry in another collection · chain C against C, TM-score 1.00
- P27001 · AlphaFold monomer V2.0 prediction for phenylalanine--tRNA ligase alpha subunit (P27001) · a predicted model of the same protein · chain A against A, TM-score 0.77
- Q5SGX2 · AlphaFold monomer V2.0 prediction for phenylalanine--tRNA ligase alpha subunit (Q5SGX2) · a predicted model of the same protein · chain B against A, TM-score 0.22
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 Q5SGX1
- Every structure of UniProt P27001
- Every structure of UniProt Q5SGX2
- Elsewhere: RCSB PDB 1EIY · PDBe 1EIY · UniProt Q5SGX1 · UniProt P27001 · UniProt Q5SGX2
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