Research workbench
Crystal structure of the complex of M. tuberculosis phers with cognate precursor tRNA and phenylalanine
Analyse Crystal structure of the complex of M. tuberculosis phers with cognate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KA0
- Type
- protein + RNA
- Length
- 2,477 residues
- Chains
- 6
- 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, K, SO4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phenylalanine--tRNA ligase alpha subunit (EC 6.1.1.20) | protein | 339 | 45% helix, 20% strand | P9WFU3 |
| B, E | Phenylalanine--tRNA ligase beta subunit (EC 6.1.1.20) | protein | 835 | 29% helix, 27% strand | P9WFU1 |
| C, F | TRNA(PHE) | rna | 66 | — | — |
| D | Phenylalanine--tRNA ligase alpha subunit (EC 6.1.1.20) | protein | 336 | 41% helix, 21% strand | P9WFU3 |
Ligands and binding sites
- PHE · Phenylalanine · ligand · 2 copies · chains A, D
- MG · Magnesium ion · metal · 12 copies · chains A, B, C, D, E, F
- K · Potassium ion · metal · 3 copies · chains B, D, E
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, D, E
- GOL · Glycerol · additive · 12 copies · chains A, B, D, E
- PGE · Triethylene glycol · additive · 3 copies · chains A, B, E, D
- ACT · Acetate ion · additive · 2 copies · chains 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 978 | 0.87 | 0.88 | 131 | empty |
| 2 | 438 | 0.79 | 0.87 | 48 | GOL, K |
| 3 | 466 | 0.79 | 0.87 | 44 | empty |
| 4 | 672 | 0.74 | 0.80 | 56 | PHE, GOL, SO4 |
| 5 | 795 | 0.74 | 0.78 | 60 | empty |
Interfaces
10 interfaces between chains.
- A–B · 4331 Ų buried · 58 hydrogen bonds · protein-protein
- D–E · 4330 Ų buried · 51 hydrogen bonds · protein-protein
- B–D · 1488 Ų buried · 21 hydrogen bonds · protein-protein
- A–E · 1479 Ų buried · 21 hydrogen bonds · protein-protein
- B–E · 1035 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7KA0 · Crystal structure of the complex of M. tuberculosis PheRS with cognate precursor tRNA and… · the same entry in another collection · chain A against A, 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 0.96
- 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 0.96
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 7KA0 · PDBe 7KA0 · UniProt P9WFU3 · UniProt P9WFU1
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