Research workbench
Crystal structure of thermus thermophilus phenylalanyl-tRNA synthetase complexed with L-dopa
Analyse Crystal structure of thermus thermophilus phenylalanyl-tRNA synthetase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TEH
- 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
- P27001, P27002
- Ligands
- DAH
- Pockets
- 16 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phenylalanyl-tRNA synthetase alpha chain (EC 6.1.1.20) | protein | 266 | 30% helix, 28% strand | P27001 |
| B | Phenylalanyl-tRNA synthetase beta chain (EC 6.1.1.20) | protein | 785 | 29% helix, 27% strand | P27002 |
Ligands and binding sites
- DAH · 3,4-dihydroxyphenylalanine · ligand · 2 copies · chains A, 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 71 | 0.72 | 0.97 | 20 | empty |
| 2 | 601 | 0.69 | 0.78 | 49 | DAH |
| 3 | 324 | 0.66 | 0.81 | 43 | DAH |
| 4 | 415 | 0.64 | 0.78 | 42 | empty |
| 5 | 56 | 0.60 | 0.91 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 4358 Ų buried · 64 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3TEH · Crystal structure of Thermus thermophilus Phenylalanyl-tRNA synthetase complexed with… · the same entry in another collection · chain A against A, 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 0.97
- P27002 · AlphaFold monomer V2.0 prediction for phenylalanine--tRNA ligase beta subunit (P27002) · a predicted model of the same protein · chain B 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 P27001
- Every structure of UniProt P27002
- Elsewhere: RCSB PDB 3TEH · PDBe 3TEH · UniProt P27001 · UniProt P27002
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