MolNFT v1 · #179568 · protein + RNA
Crystal structure of the complex of M. tuberculosis phers with cognate precursor tRNA and 5'-O-(N-PHENYLALANYL)SULFAMOYL-adenosine
7K9M · Phenylalanine--tRNA ligase alpha subunit: “Crystal structure of the complex of M. tuberculosis phers with cognate precursor tRNA and…”. X-ray diffraction, 2 ligands (W5Y, MG), 17 pockets (best druggability 0.79). MolNFT v1 #179568…
- PDB
- 7K9M
- Type
- protein + RNA
- Length
- 1,239 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
- W5Y, MG
- Pockets
- 17 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phenylalanine--tRNA ligase alpha subunit (EC 6.1.1.20) | protein | 339 | 44% helix, 21% strand | P9WFU3 |
| B | Phenylalanine--tRNA ligase beta subunit (EC 6.1.1.20) | protein | 834 | 29% helix, 27% strand | P9WFU1 |
| C | TRNA(PHE) | rna | 66 | — | — |
Ligands and binding sites
- W5Y · 5'-O-(L-phenylalanylsulfamoyl)adenosine · ligand · chains A
- MG · Magnesium ion · metal · 3 copies · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B
- P6G · Hexaethylene glycol · additive · chains A, B
- PGE · Triethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 486 | 0.79 | 0.87 | 47 | GOL |
| 2 | 640 | 0.75 | 0.81 | 64 | W5Y, GOL |
| 3 | 305 | 0.68 | 0.82 | 30 | empty |
| 4 | 303 | 0.68 | 0.83 | 55 | empty |
| 5 | 315 | 0.67 | 0.82 | 31 | GOL |
Interfaces
3 interfaces between chains.
- A–B · 4427 Ų buried · 58 hydrogen bonds · protein-protein
- B–C · 438 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–C · 434 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 7K9M · Crystal structure of the complex of M. tuberculosis PheRS with cognate precursor tRNA and… · 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 0.94
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 P9WFU3
- Every structure of UniProt P9WFU1
- Elsewhere: RCSB PDB 7K9M · PDBe 7K9M · UniProt P9WFU3 · UniProt P9WFU1
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