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The crystal structure of a putative phenylalanyl-tRNA synthetase (phers) beta chain domain from bacteroides fragilis to 2.1A
Analyse The crystal structure of a putative phenylalanyl-tRNA synthetase (phers) beta… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IG2
- Type
- protein
- Length
- 768 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phenylalanyl-tRNA synthetase beta chain
- EC
- 6.1.1.20
- UniProt
- Q64T65
- Ligands
- MG
- Pockets
- 10 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phenylalanyl-tRNA synthetase beta chain (EC 6.1.1.20) | protein | 190 | 34% helix, 35% strand | Q64T65 |
| B | Phenylalanyl-tRNA synthetase beta chain (EC 6.1.1.20) | protein | 197 | 31% helix, 34% strand | Q64T65 |
| C | Phenylalanyl-tRNA synthetase beta chain (EC 6.1.1.20) | protein | 187 | 34% helix, 29% strand | Q64T65 |
| D | Phenylalanyl-tRNA synthetase beta chain (EC 6.1.1.20) | protein | 194 | 30% helix, 30% strand | Q64T65 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 429 | 0.73 | 0.83 | 50 | empty |
| 2 | 317 | 0.56 | 0.76 | 42 | empty |
| 3 | 124 | 0.47 | 0.78 | 18 | empty |
| 4 | 148 | 0.46 | 0.77 | 25 | empty |
| 5 | 137 | 0.46 | 0.77 | 25 | empty |
Interfaces
4 interfaces between chains.
- A–D · 1063 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 422 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 128 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 83 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 3IG2 · The Crystal Structure of a Putative Phenylalanyl-tRNA synthetase (PheRS) beta chain… · the same entry in another collection · chain D against D, TM-score 1.00
- Q64T65 · AlphaFold monomer V2.0 prediction for phenylalanine--tRNA ligase beta subunit (Q64T65) · a predicted model of the same protein · chain C 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 Q64T65
- Elsewhere: RCSB PDB 3IG2 · PDBe 3IG2 · UniProt Q64T65
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