Research workbench
Crystal structure of mycobacterium tuberculosis phenylalanyl-tRNA synthetase in complex with compound GDI05-001
Analyse Crystal structure of mycobacterium tuberculosis phenylalanyl-tRNA synthetase in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DB7
- Type
- protein
- Length
- 1,103 residues
- Chains
- 2
- 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
- H2L, SO4
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phenylalanine--tRNA ligase alpha subunit (EC 6.1.1.20) | protein | 267 | 32% helix, 27% strand | P9WFU3 |
| B | Phenylalanine--tRNA ligase beta subunit (EC 6.1.1.20) | protein | 836 | 28% helix, 27% strand | P9WFU1 |
Ligands and binding sites
- H2L · 1-[3-[2-(1H-indol-3-yl)ethylsulfamoyl]phenyl]-3-(1,3-thiazol-2-yl)urea · ligand · chains A
- SO4 · Sulfate ion · ion · 12 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 468 | 0.78 | 0.86 | 54 | SO4 |
| 2 | 859 | 0.75 | 0.79 | 70 | H2L, SO4 |
| 3 | 194 | 0.66 | 0.85 | 25 | empty |
| 4 | 417 | 0.65 | 0.78 | 41 | SO4 |
| 5 | 258 | 0.63 | 0.81 | 32 | SO4 |
Interfaces
1 interface between chains.
- A–B · 4358 Ų buried · 48 hydrogen bonds · protein-protein
Compared structures
- 7DB7 · Crystal structure of Mycobacterium tuberculosis phenylalanyl-tRNA synthetase in complex… · 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 0.95
- 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 7DB7 · PDBe 7DB7 · UniProt P9WFU3 · UniProt P9WFU1
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