Research workbench
Escherichia COLI tRNA synthetase
Analyse Escherichia COLI tRNA synthetase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P24
- Type
- protein
- Length
- 2,151 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phenylalanine--tRNA ligase alpha subunit; Phenylalanine--tRNA ligase beta subunit
- EC
- 6.1.1.20
- UniProt
- P08312, P07395
- Ligands
- MG, CL
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phenylalanine--tRNA ligase alpha subunit (EC 6.1.1.20) | protein | 241 | 32% helix, 27% strand | P08312 |
| B | Phenylalanine--tRNA ligase beta subunit (EC 6.1.1.20) | protein | 793 | 26% helix, 29% strand | P07395 |
| C | Phenylalanine--tRNA ligase alpha subunit (EC 6.1.1.20) | protein | 323 | 44% helix, 20% strand | P08312 |
| D | Phenylalanine--tRNA ligase beta subunit (EC 6.1.1.20) | protein | 794 | 27% helix, 30% strand | P07395 |
Ligands and binding sites
- MG · Magnesium ion · metal · 13 copies · chains A, B, D, C
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 17 copies · chains A, B, D, C
- PEG · Di(hydroxyethyl)ether · additive · 10 copies · chains A, B, D, C
- HEZ · Hexane-1,6-diol · additive · 5 copies · chains A, B, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, B, D, C
- PGE · Triethylene glycol · additive · 2 copies · chains B, A, 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 771 | 0.82 | 0.85 | 74 | TRS, MG, PEG, EDO |
| 2 | 1093 | 0.78 | 0.80 | 91 | TRS, PGE, EDO, HEZ, PEG |
| 3 | 871 | 0.77 | 0.80 | 80 | EDO, MG |
| 4 | 349 | 0.76 | 0.87 | 30 | empty |
| 5 | 832 | 0.75 | 0.79 | 71 | EDO |
Interfaces
6 interfaces between chains.
- C–D · 3682 Ų buried · 60 hydrogen bonds · protein-protein
- A–B · 3598 Ų buried · 61 hydrogen bonds · protein-protein
- B–C · 2020 Ų buried · 41 hydrogen bonds · protein-protein
- A–D · 1915 Ų buried · 40 hydrogen bonds · protein-protein
- B–D · 1303 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 6P24 · Escherichia coli tRNA synthetase · the same entry in another collection · chain D against D, TM-score 1.00
- P08312 · AlphaFold monomer V2.0 prediction for phenylalanine--tRNA ligase alpha subunit (P08312) · a predicted model of the same protein · chain A against A, TM-score 0.97
- 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 0.94
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 P08312
- Every structure of UniProt P07395
- Elsewhere: RCSB PDB 6P24 · PDBe 6P24 · UniProt P08312 · UniProt P07395
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