Research workbench
M. tuberculosis phers complex with cognate precursor tRNA and phenylalanine
Analyse M. tuberculosis phers complex with cognate precursor tRNA and phenylalanine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KAB
- Type
- protein + RNA
- Length
- 1,236 residues
- Chains
- 3
- 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
- P9WFU3, P9WFU1
- Ligands
- PHE, MG, SO4
- Pockets
- 18 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phenylalanine--tRNA ligase alpha subunit (EC 6.1.1.20) | protein | 335 | 41% helix, 21% strand | P9WFU3 |
| B | Phenylalanine--tRNA ligase beta subunit (EC 6.1.1.20) | protein | 835 | 28% helix, 27% strand | P9WFU1 |
| C | TRNA(PHE) | rna | 66 | — | — |
Ligands and binding sites
- PHE · Phenylalanine · ligand · chains A
- MG · Magnesium ion · metal · 10 copies · chains A, B, C
- SO4 · Sulfate ion · ion · chains A, B
- PGR · R-1,2-propanediol · additive · 3 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
- PGO · S-1,2-propanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 470 | 0.78 | 0.86 | 48 | GOL, PGR |
| 2 | 674 | 0.73 | 0.79 | 52 | PHE, GOL, MG, SO4 |
| 3 | 908 | 0.70 | 0.76 | 53 | MG |
| 4 | 275 | 0.65 | 0.82 | 29 | empty |
| 5 | 214 | 0.63 | 0.83 | 27 | empty |
Interfaces
3 interfaces between chains.
- A–B · 4358 Ų buried · 57 hydrogen bonds · protein-protein
- A–C · 437 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–C · 422 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 7KAB · M. tuberculosis PheRS complex with cognate precursor tRNA and phenylalanine · the same entry in another collection · chain C against C, TM-score 1.00
- P9WFU1 · AlphaFold monomer V2.0 prediction for phenylalanine--tRNA ligase beta subunit (P9WFU1) · a predicted model of the same protein · chain B against A, TM-score 0.95
- P9WFU3 · AlphaFold monomer V2.0 prediction for phenylalanine--tRNA ligase alpha subunit (P9WFU3) · 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 P9WFU3
- Every structure of UniProt P9WFU1
- Elsewhere: RCSB PDB 7KAB · PDBe 7KAB · UniProt P9WFU3 · UniProt P9WFU1
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