Research workbench
Prolyl-tRNA synthetase from thermus thermophilus complexed with TRNAPRO(CGG) and a prolyl-adenylate analogue
Analyse Prolyl-tRNA synthetase from thermus thermophilus complexed with TRNAPRO(CGG)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1H4S
- Type
- protein + RNA
- Length
- 1,013 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prolyl-tRNA synthetase; TRNAPRO(CGG)
- EC
- 6.1.1.15
- Ligands
- PSD, ZN, SO4
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Prolyl-tRNA synthetase (EC 6.1.1.15) | protein | 473 | 39% helix, 30% strand | — |
| T | TRNAPRO(CGG) | rna | 67 | — | — |
Ligands and binding sites
- PSD · 5'-O-[N-(prolyl)-sulfamoyl]adenosine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1030 | 0.78 | 0.80 | 78 | empty |
| 2 | 663 | 0.75 | 0.81 | 60 | empty |
| 3 | 532 | 0.73 | 0.81 | 46 | PSD, SO4 |
| 4 | 539 | 0.72 | 0.81 | 50 | PSD, SO4 |
| 5 | 186 | 0.60 | 0.82 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2114 Ų buried · 31 hydrogen bonds · protein-protein
- B–T · 867 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–T · 404 Ų buried · 11 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 1H4S · Prolyl-tRNA synthetase from Thermus thermophilus complexed with tRNApro(CGG) and a… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 1H4S · PDBe 1H4S
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