MolNFT v1 · #67164 · protein
The crystal structure of the beta subunit of a phenylalanyl-tRNA synthetase from porphyromonas gingivalis W83
3ICA · Phenylalanyl-tRNA synthetase beta chain: “The crystal structure of the beta subunit of a phenylalanyl-tRNA synthetase from porphyromonas gingivalis W83”. X-ray diffraction, 1 ligand (TAM), 4 pockets (best druggability 0.80). MolNFT…
- PDB
- 3ICA
- Type
- protein
- Length
- 412 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phenylalanyl-tRNA synthetase beta chain
- EC
- 6.1.1.20
- UniProt
- Q7MXR4
- Ligands
- TAM
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phenylalanyl-tRNA synthetase beta chain (EC 6.1.1.20) | protein | 205 | 31% helix, 34% strand | Q7MXR4 |
| B | Phenylalanyl-tRNA synthetase beta chain (EC 6.1.1.20) | protein | 207 | 31% helix, 33% strand | Q7MXR4 |
Ligands and binding sites
- TAM · Tris(hydroxyethyl)aminomethane · ligand · chains A, B
- GOL · Glycerol · additive · 11 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 338 | 0.80 | 0.90 | 57 | GOL, TAM |
| 2 | 307 | 0.59 | 0.78 | 55 | GOL |
| 3 | 126 | 0.41 | 0.75 | 23 | empty |
| 4 | 95 | 0.38 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1495 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 3ICA · The crystal structure of the beta subunit of a phenylalanyl-tRNA synthetase from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q7MXR4 · AlphaFold monomer V2.0 prediction for phenylalanine--tRNA ligase beta subunit (Q7MXR4) · a predicted model of the same protein · chain A 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 Q7MXR4
- Elsewhere: RCSB PDB 3ICA · PDBe 3ICA · UniProt Q7MXR4
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