MolNFT v1 · #179582 · protein + RNA
Crystal structure of the complex of M. tuberculosis phers with cognate precursor tRNA and phenylalanine
7KA0 · Phenylalanine--tRNA ligase alpha subunit: “Crystal structure of the complex of M. tuberculosis phers with cognate precursor tRNA and phenylalanine”. X-ray diffraction, 4 ligands (PHE, MG, K), 20 pockets (best druggability 0.87).…
- 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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