Research workbench
Crystal structure of E. COLI phenylalanine-tRNA synthetase complexed with phenylalanine and AMP
Analyse Crystal structure of E. COLI phenylalanine-tRNA synthetase complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PCO
- Type
- protein
- Length
- 2,155 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phenylalanyl-tRNA synthetase, alpha subunit; Phenylalanyl-tRNA synthetase, beta chain
- UniProt
- C9QTZ3, P07395
- Ligands
- PHE, AMP
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phenylalanyl-tRNA synthetase, alpha subunit | protein | 242 | 29% helix, 23% strand | C9QTZ3 |
| B, D | Phenylalanyl-tRNA synthetase, beta chain | protein | 795 | 22% helix, 25% strand | P07395 |
| C | Phenylalanyl-tRNA synthetase, alpha subunit | protein | 323 | 30% helix, 18% strand | C9QTZ3 |
Ligands and binding sites
- PHE · Phenylalanine · ligand · 2 copies · chains A, C
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, 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 | 1015 | 0.84 | 0.85 | 100 | empty |
| 2 | 1070 | 0.78 | 0.80 | 82 | empty |
| 3 | 1172 | 0.78 | 0.80 | 80 | empty |
| 4 | 652 | 0.74 | 0.81 | 72 | PHE, AMP |
| 5 | 674 | 0.74 | 0.80 | 68 | PHE, AMP |
Interfaces
6 interfaces between chains.
- C–D · 3620 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 3524 Ų buried · 50 hydrogen bonds · protein-protein
- B–C · 2093 Ų buried · 33 hydrogen bonds · protein-protein
- A–D · 2060 Ų buried · 31 hydrogen bonds · protein-protein
- B–D · 1338 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 3PCO · crystal structure of E. coli phenylalanine-tRNA synthetase complexed with phenylalanine… · the same entry in another collection · chain A against A, TM-score 1.00
- P07395 · AlphaFold monomer V2.0 prediction for phenylalanine--tRNA ligase beta subunit (P07395) · a predicted model of the same protein · chain D against A, TM-score 0.95
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 C9QTZ3
- Every structure of UniProt P07395
- Elsewhere: RCSB PDB 3PCO · PDBe 3PCO · UniProt C9QTZ3 · UniProt P07395
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